The Model Context Protocol (MCP), which was launched recently by Anthropic, quickly became the standard for connecting AI models to diverse sources of data and tools. Its effectiveness was so powerful that OpenAI, along with other major AI giants and some of the popular hyperscalers, too, have adopted it. Within a few months, MCP experienced a huge growth. Vendors across the world now offer thousands of MCP servers by allowing AI assistants to integrate with enterprise data and services seamlessly.

As Agentic AI becomes the future of IT, adoption of MCP and related protocols is growing across enterprises. However, as security teams and organizations race to deploy AI, they have started to notice that even innovations like MCP also come with significant vulnerabilities.

This blog highlights the significant vulnerabilities of the Model Context Protocol and its impact on enterprises.

Common MCP Security Vulnerabilities

Here’s a breakdown of some of the common MCP vulnerabilities

Authentication Flaws

The 2025-06-18 MCP specification mandates OAuth 2.1 proper token validation and secure session management. But still, many MCP servers remain exposed with a lack of strong authentication, misconfigured OAuth, plain-text token storage, and poor session controls. This authentication flaw is further expanded by old static OAuth client IDs that allow cookie replay to bypass user consent. Attackers can misuse unauthenticated endpoints, steal service tokens or use expired tokens because of weak validation. This flaw compromises the security, which leaves sensitive data and operations vulnerable to compromise. Quick remediation needs enforcing OAuth 2.1 requirements, secure token storage and implementing strong session management

Data Leakage

Data leakage happens through an MCP output-layer, where an agent accidentally leaks sensitive data such as internal IDs, infrastructure details, or user data in its final response. This leak often occurs from excessive broad tool outputs, the absence of filtering logic, or the blind inclusion of retrieved context without validation. The risk level is usually high and can lead to breach of compliance, privacy violations and exploitation of leaked system details. Remediation for this vulnerability includes strict output sanitization, applying RBAC control to tool outputs before resurfacing them, and enforcing automated tests to detect and redact sensitive data before final responses.

Insecure APIs or Interfaces

MCP servers built from API specifications have a risk of inheriting risks or flaws from incomplete or low-quality specifications, such as absent endpoints, unclear parameter definitions, and insufficient input validation. Unlike the conventional REST APIs, MCP servers lack mature security patterns, testing frameworks and best security practices, which leads to vulnerabilities initially. Weak API specs increase the probability of weak integrations and exploitable security gaps. Since MCPs inherit flaws from poor API specifications, they align closely with some of the key OWASP API risks such as.

• Broken Object Level Authorization: Unclear endpoint definitions that results in MCP agents accessing the unauthorized data.

• Unrestricted Resource Consumption: Weak parameter documentation enables unnecessary requests which can cause server overload.

• Improper Inventory Management: Outdated or unclear documentation conceals exposed endpoints from monitoring.

• Misconfigured Security: Poor defaults and missing secure settings put the MCP server at risk of attacks.

Insufficient Encryption

In MCP deployments, insufficient encryption happens when servers transfer the data without any secure protocols like SSL, TLS. This absence of protocols can result in the exposure of sensitive data to interception and tampering during transfer. A recent analysis found hundreds of MCP servers running without TLS or SSL, which left all the data exchanges, client commands, API tokens and credentials exposed and unsecured. Unencrypted traffic often makes these servers prone to Man-in-the-Middle (MitM) attacks. This is where a cyber attacker can intercept, read, or even manipulate communication between the client & server, which potentially allows the injection of harmful commands or the theft of data.

Improper Access Controls

MCP integrations usually request more permissions than needed, which violates the principle of least privilege. This broad access request, combined with centralized access tokens, increases the impact of compromise. Excessive permissions allow complete read or write access to the database instead of read-only, which gives too much exposure. Without strong RBAC, a weak MCP server can allow full-fledged access across connected systems. Insufficient audit logs make it challenging to identify excess permissions. Furthermore, malicious access patterns or unauthorized updates/changes could go unnoticed until big damage happens, if there is no implementation of efficient logging.

Zero-Day Exploits

MCP experiences both documented and evolving zero day vulnerabilities. A zero-day exploit in MCP is a vulnerability used by attackers in real-world attacks, the moment it is discovered before developers are aware of the vulnerability or have released a patch. This attack mainly targets MCP servers, tools and protocols. A recent issue where CVE-2025-49596 allowed unauthenticated RCE in the MCP inspector, which got fixed in v0.14.1 through origin checks and strong authentication. A broader zero-day vulnerability includes tool poisoning, schema manipulation, and cross-server data exfiltration. To mitigate, promptly update vulnerable components, apply OAuth-based identity verification, and implement RBAC controls. Besides this, regular and secure third-party tool evaluation helps protect against undiscovered MCP protocol vulnerabilities.

How to Identify MCP Vulnerabilities

You can identify MCP vulnerabilities via multiple methods, including some proven methods, to effectively identify vulnerabilities before they cause significant risks.

Security Testing Platforms

To detect MCP vulnerabilities, use security platforms like Akto MCP security platform, Burp Suite, OWASP ZAP, and OpenVAS to automatically test for misconfigurations, outdated components, and other flaws. Perform penetration testing quarterly to simulate real-world attacks on servers, connectors and APIs. Continuously review audit logs to detect threats, such as malicious patterns like suspicious schema changes, unauthorized tool registrations, repeated failed logins, or large outbound data transfers. Apply anomaly detection to flag unusual patterns in real time. Therefore, combining proactive, continuous log monitoring and simulated attacks to discover emerging threats and vulnerabilities before they can be exploited.

Penetration Testing

Penetration testing mimics attacker methods to expose weaknesses in MCP components, which include APIs, connectors, and authentication flows, ensuring they are fixed before exploitation. Besides this, test quarterly and again after making changes to MCP architecture or security controls, increase the frequency for crucial high-risk workloads.

Audit Logs & Anomaly Detection

Audit logs are essential for tracking MCP actions, which include authentication events, tool executions, connector registrations, and schema changes. Consistent log analysis helps identify suspicious patterns initially. Furthermore, anomaly detection flags suspicious attack surface from normal usage, which is crucial for identifying zero-day exploits.

Best Practices for Mitigating MCP Vulnerabilities

Minimize MCP vulnerabilities by applying the best practices below to ensure sustained MCP security.

Implement Strong Authentication & Authorization

MCP Security can be strengthened by assigning authentication to trusted OAuth 2.1 identity providers, which can enforce multi-factor authentication via PKCE secured flows and metadata-driven discovery. The protocol also supports fine-grained authorization. MCP clients must request clear permissions, such as read or write files. Along with this, MCP servers should validate the scope before allowing access. This approach ensures that agents get the least privilege necessary to perform their actions. Therefore, by implementing temporary, scope-limited tokens and limited authorization, MCP lowers the attack surface and follows the principle of least privilege access.

Regular Patch Management

Regular patch management is crucial for protecting MCP environments. Automate patch cycles by integrating MCP server and client updates into CI/CD pipelines or through configuration tools to ensure prompt fixes. Continuously monitor databases of CVE and security feeds, such as GitHub advisories, for MCP vulnerabilities. Such as CVE-2025-49596 (Anthropic MCP inspector RCE), CVE-2025-6514 (MCP-Remote RCE), CVE-2025-53818 (GitHub Kanban MCP injection) and implement vendor patches to tackle the exposure.

Secure Configuration Management

Secure configuration management in MCP needs strong server hardening and proactive drift prevention. Apply isolation by containerizing MCP servers using non-root users, kernel namespace, and read-only filesystems. Implement least-privilege access, input validation, output sanitization, and mutual authentication between components. Consistently maintain dynamic credential hygiene, avoid hard-coded secrets, and rotate them using tools like AWS STS or Vault. Automate checks for configuration and baseline compliance through CI/CD infrastructure-as-code for audits. Centralize logging and integrate threat detection to find unauthorized modifications early. Secure configuration ensures MCP systems remain both strong and resilient.

Conduct Routine Security Audits

Security teams must conduct thorough routine internal audits to evaluate MCP deployments against internal policies that prioritize memory usage, context flows, and access control consistency. Combine this with external audits by independent evaluators to verify adherence to standards such as SOC 2 or ISO 27001 and reinforce trust. Finally, maintain extensive documentation such as audit reports, context flow logs, change history, and schematic diagrams to assist in forensic analysis and continuous improvement. Match audit process with regulatory requirements and compliance to ensure transparency and strong governance.

Real World Example of MCP Vulnerability CVE-2025-6514

A critical OS vulnerability was found in the mcp-remote tool. The MCP remote tool is used to connect local applications to remote MCP servers. Versions 0.0.5 to 0.1.15 were impacted. During the authorization, malicious MCP servers could send specially designed URLs to the client. This happened because mcp-remote was blindly running these URLs using the underlying OS interpreter, attackers could trigger RCE (remote code execution) on the developer’s system. This resulted in a complete system compromise, and the flaw was fixed or patched in version 0.1.16.

Image Source: MCP Vulnerability by William OGOU

Cyber attackers utilized a seemingly safe authorization endpoint URL integrating the OS commands. When mcp-remote tried to open it through PowerShell on Windows, the embedded payload began to run automatically. This compact mechanism made the exploit significantly effective with a simple server response.

This incident highlights the risks of trusting external outputs, particularly in agentic systems like MCP. Key takeaways from this real-world incident are.

1. Perform timely updates when patches are released.

2. Mandatorily sanitize and validate external inputs.

3. Identify toolchain vulnerabilities in ecosystem agents outside backend servers.

It also explains how seemingly safe developer tools can turn into attack vectors and result in full compromise. Also, the incident highlights the need for strong input validation and prioritizing security across all MCP components.

Final Thoughts

Overall, security teams and organizations need to ensure MCP implementations comply with regulatory standards combined with best practices and effective mitigation strategies to prevent and tackle any new attack vectors and vulnerabilities. Akto, with its industry-first MCP security, is designed to protect Model Context Protocol servers with capabilities such as MCP server discovery, full endpoint visibility, live threat detection, real-time monitoring, deep vulnerability testing, and more. Akto security solutions are created for modern AI stacks, which let you identify shadow MCPs, audit AI agent activity, and help security teams tackle risks and significant vulnerabilities right from the initial stage.

Looking to strengthen your API and MCP defense mechanism? Connect with Akto security experts today!