Model Context Protocol (MCP) is evolving and making headlines in the AI sector since its introduction in late 2024. However, with this innovation comes a new wave of security risks that security teams cannot ignore. As per recent report, a team of security researchers have identified a growing number of security risks in MCP servers, by calling them a “significant security concerns” for security teams. As business organizations integrate MCPs into their workflows, attackers are exploiting new vulnerabilities that are unique to these protocols.

This blog highlights the Top 10 security risks of Model Context Protocol and offers insights to protect AI-driven operations.

What are Model Context Protocol (MCP) Security Risks?

MCP security risks are the potential vulnerabilities and dangers that are associated with the use of Model Context Protocol (MCP). MCP is a technology that allows AI models to interact with external tools, services or databases to perform activities and retrieve information. In other words, MCP security risks are possible vulnerabilities that can occur, if MCP is not properly protected, which makes it easier for attackers to misuse AI driven systems.

10 Critical MCP Security Risks in 2025 and How to Protect Your AI Systems

Here’s a breakdown of top 10 MCP security risks that every AI-powered organizations must be aware of:

Misconfiguration and Policy Drift in MCP

Misconfigurations occur when MCP servers or AI agents are set up with lack of secure or excessive permissions mostly because of impulsive deployments without proper security review. This approach can lead AI agents into a potential entry point for attackers. On the other hand, policy drift occurs when security settings become outdated or inconsistent over time, especially with periodic changes or upgraded integrations. This approach can lead to undocumented access paths which attackers can exploit.

Root causes for misconfiguration and policy drift:

1. When there are barely any security review

2. Inadequate monitoring

3. Lack of standardization authentication

4. Excessive permissions

Mitigation Solution:

To prevent this risk, security teams should perform regular and vigorous security review, strong access controls, periodic audits and principle of least privilege to make sure MCP integrations remain protected.

Privilege Escalation via AI Agents

Privilege escalation through AI agents happens in MCP when attackers manipulate the AI agents to gain broad access rights than intended, which allows them to conduct unauthorized actions or get access to sensitive or confidential data and systems.

Root causes for privilege escalation:

1. Over permissions to AI agents

2. Lack of sufficient validation of context metadata and prompts

3. Poor authentication and identity management

4. Lack of role based access controls (RBAC)

Mitigation Solution:

To prevent such risks security teams should impose strict access controls and continuous monitoring to make sure AI agents function within the limited boundaries.

Insufficient Audit and Explainability

Insufficient audit and Explainability in MCP is when business organizations do not equip themselves with enough detailed records and transparency about what AI agents are doing. This approach makes it challenging to trace actions, understand or investigate incidents.

Root causes for insufficient audit and explainability are:

1. Limited logging of activities

2. Lack of audit frameworks

3. Rapid deployment of MCP

4. Insufficient tools to provide transparency on AI decisions and actions

Mitigation Solution:

security teams should Implement audit logging for all MCP and agent activities, regularly perform log reviews and utilize them for security monitoring, compliance and incident response.

Bypass via Shadow APIs or Agent Channels

Bypassing through shadow API’s or agents channels involves attackers exploiting or misusing the undocumented, unmonitored or unofficial API’s and hidden interaction channels between agents to bypass the security controls in a MCP setting.

Root causes for bypassing through shadow API:

1. Legacy testing endpoints

2. Unauthorized deployments

3. Over permissive defaults

Mitigation solution:

Security teams must ensure integrated MCP validation checks into CI/CD pipelines using tools like security composition analysis to identify and monitor shadow deployments, and enforce least privilege permissions.

Insider Threats with Elevated Access

Insider threats in MCP involves risks that are faced by individuals within the organizations (insiders) such as employees, contractors or administrators who have privileges of higher access to MCP servers, agents configurations or integrations. These insiders can accidentally or intentionally misuse their privileges of higher access which can cause comprised systems, accidental or intentional data leakage, and unauthorized actions.

Root causes for insider threats with elevated access:

1. Lack of granular access controls

2. Insufficient monitoring

3. Absence of auditing

4. Broad centralized access

Mitigation solution:

To prevent such risks security teams must conduct regular security awareness training, regular reviews of access rights, immediate revocation of unnecessary privileges and deploy continuous monitoring.

Zero-Day Exploits on MCP Software & Firmware

Zero-day exploits are security risks that target previously unknown vulnerabilities in MCP software which allows attackers to compromise systems before a patch is available. This occurs when MCP bridges role between AI models and internal systems that allows a broad attack surface, particularly when open-source code is used.

Root causes for Zero-Day Exploit:

1. Rapid integration of MCP

2. Lack of thorough security review

3. Lack of authentication and insecure connectors

4. Poor input validation

Mitigation Solution:

To avoid such risks security teams must strictly audit MCP deployments, enforce strict access controls, input validation, and authentication. Also, should update and patch MCP software regularly and include MCP in all the threat modeling and pen testing practices to identify protocol-level risks at the earliest.

Data Leakage in Multi-Cloud / Hybrid Environments

Data leakage in multi-cloud or hybrid environments occurs when unintended exposure or transfer of sensitive data across various on-premises systems, cloud providers or external tools happen through MCP. This risk is increased as MCP acts as a bridge by allowing AI models and agents to access and move data between multiple environments, which leads to attack surface, attackers can misuse weaknesses in one environment to access data across various clouds or on-premises systems.

Root causes for Data Leakage are:

1. Complex integrations

2. Inconsistent security policies

3. Inadequate context validation

4. Poor management of credentials or tokens

Mitigation Solution: To prevent such risks security teams must strictly implement Context-Based Access Controls, have consistent security policies in place, enforce strong encryption for data in transit and at rest, and authentication for all MCP interactions. Besides this, constantly monitor audit data flows and MCP activities.

Insecure Inter-Agent Communications

Insecure inter-agent communications in MCP occur when AI agents and MCP servers exchange commands or data over channels that does not have proper encryption, authentication, or monitoring. This issue exposes the system to manipulation and unauthorized access as agents share sensitive data.

Root causes for insecure Inter-Agent Communications:

1. Because of impulsive deployment of new agents.

2. Excessive permissions and inadequate access controls.

3. Lack of strong authentication and encryption between agents and MCP servers.

Mitigation Solution: Conduct regular audit and monitor agent interactions of shadow channels. Implement encryption, mutual authentication for all agent communications in MCP environments. Apply the principle of least privilege and use secure connectors and implement strong input and output validation to prevent data exfiltration and command injection.

Lack of Redundancy and Resilience

Lack of redundancy and resilience in MCP is basically when the protocol’s infrastructure is not created to tolerate failures. If a key MCP component (host, client, or server) experience failure, there might be no backup which eventually results in service outages or reduced AI functionality. These outages can disturb the normal business operations, especially when MCP connects the real-time data sources.

Root causes for lack of redundancy and resilience:

1. Due to excess reliance on single instances of components without built-in redundancy.

2. Absence of proper backup mechanism.

3. Ineffective monitoring and automated recovery processes

Mitigation Solution: To prevent this issue, security teams should deploy multiple instances of MCP components across different zones for backup, automatically reroute requests in case a component fails, monitor all MCP components for performance, and automate alerts for rapid incident response.

Delayed or Ineffective Incident Response

Delayed or ineffective incident response is a lack of mechanism to detect, analyze, and mitigate security incidents quickly within MCP driven environments. This security risk can result in extended exposure, major damage, and lost opportunities to recover systems. Apart from this the distributed nature of MCP deployments can make incident response too slow.

Root causes for delayed or ineffective incident Response:

1. There are no contextual awareness and real-time monitoring.

2. Inadequate integration between MCP and automated incident management tools.

3. Limited explainability which makes it challenging to understand & identify root causes.

Mitigation Solution:

To mitigate this risk security teams must integrate MCP with incident management tools for real-time detection, intelligent routing of incidents and implement logging and monitoring for all the MCP activities. Use context-aware automation to detect potential failure points and actively mitigate risks before they cause damage.

Final Thoughts

With over hundreds Model Context Protocol (MCP) servers live, it has unlocked real time AI automation. However, it also brings along a bunch of serious new security risks. To prevent and tackle them, Akto has introduced industry first MCP Security Platform for AppSec teams. It is designed to protect Model Context Protocol servers with its capabilities like MCP server discovery, full endpoint visibility, live threat detection, real time monitoring, deep vulnerability testing and more.

Akto helps you shield MCP servers and APIs from top security risks.

Connect with Akto security experts today to explore more on MCP security and API Security.