Day 12: The Anthropic’s MCP as a Data Agent - Security (Part 7)

100 days of Agentic AI: From foundations to Autonomous workflows

MCP as a Data Agent

• Central Concept: The MCP server becomes a “data agent” for an LLM, providing external tools, data, and services in a standardized, secure manner.
• Core Idea: The LLM can invoke various capabilities (like code execution, web searches, or database queries) through the MCP server, effectively extending the model’s functionality.

MCP’s Typical Lifecycle Phases

1. Initialization (Handshake)

• Client Connection: The client connects to the MCP server.
• Capability Exchange: They share lists of supported tools, resources, and protocol versions.
• Example: The server advertises a “web search” tool, while the client indicates it can handle JSON-RPC 2.0 requests.

2. Operational Phase

• JSON-RPC Method Calls: The client invokes tools or requests data (invoke_tool, get_resource) as needed by the LLM’s prompts.
• Server Execution: The MCP server processes requests, returns results, or sends notifications when new data/resources become available.
• Example: An LLM coding assistant calls invoke_tool to run a compiler, then get_resource to fetch relevant documentation.

3. Shutdown

• Session Closure: The client signals the server to terminate the session.
• Resource Cleanup: Any allocated resources or temporary artifacts are safely released.
• Example: After finishing a conversation or task, the client ends the session, preventing lingering processes or open connections.

Security Concerns across the lifecycle

• Open-Ended Tool Invocation: Allows for potentially harmful actions (e.g., malicious code execution or unauthorized data access).

Threat Mitigation:

• Access Tokens & Validation on every request.
• Sandboxing Tool Execution to prevent system-wide harm.
• Optional Decentralized IDs (DIDs) for robust identity checks.
• Example: A suspicious prompt injection attempt triggers the server’s policy checks, resulting in a blocked action or an error response.

Threat 1: Installer Spoofing | Phase: Creation

Attackers distribute a fake installer or MCP component that appears legitimate, tricking users into installing malicious software or compromised libraries.

Mitigation Plan

• Sign all installers with a trusted certificate and validate the signature before installation.
• Provide checksums or hashes on a secure website so users can verify integrity.
• Maintain a central registry of approved versions and release channels.

Example

• A developer downloads what they believe is the official MCP server installer from a phishing site. After installation, their environment is infected, allowing remote access or data theft.

Sample Code / Config

#!/usr/bin/env bash
# verify_install.sh
# 1) Import official public key
curl -sS -O https://example.com/mcp-signing-publickey.gpg
gpg --import mcp-signing-publickey.gpg

# 2) Download installer + signature
curl -sS -O https://example.com/mcp_installer.bin
curl -sS -O https://example.com/mcp_installer.sig

# 3) Verify signature
gpg --verify mcp_installer.sig mcp_installer.bin

# (Optional) Check SHA-256 checksum
sha256sum -c mcp_installer.bin.sha256

# If all good, run the installer
chmod +x mcp_installer.bin
./mcp_installer.bin

Threat 2: Supply-Chain Backdoors | Phase: Creation

Threat

• Malicious code or backdoors introduced into MCP tool dependencies, libraries, or third-party modules, compromising the entire chain.

Mitigation Plan

• Maintain a Software Bill of Materials (SBOM) for all MCP components.
• Require code signing for critical libraries and use a trusted repository with strict controls.
• Perform regular audits and security scans on dependencies (e.g., static code analysis).

Example

• A routine update to a library used by the MCP server contains a hidden credential-stealing function inserted by a rogue maintainer.

Threat 3: Name Collision | Phase: Creation

Threat

• Two tools or resources with the same name cause confusion or unintentional overwriting of one another, leading to unexpected behavior or security gaps.

Mitigation Plan

• Implement a namespace or scoped naming convention (e.g., org.user.toolName).
• Enforce unique IDs or version tagging for each tool when registering with the MCP server.
• Validate that newly registered tool/resource names don’t clash with existing ones.

Example

• A developer registers a “database_query” tool, unaware that “database_query” already exists. Calls intended for one tool end up hitting the other.

Threat 4: No Auth Handshake | Phase: Creation

Threat

• The client and server skip authentication during the initial handshake, allowing unauthorized or man-in-the-middle parties to impersonate legitimate participants.

Mitigation Plan

• Require token exchange, OAuth flow, or mutual TLS during handshake.
• Validate client identity (e.g., using a client certificate or DID-based signature).
• Terminate the connection if authentication fails or is missing.

Example

• A user sets up an MCP server with “handshake optional.” Attackers discover the open endpoint and masquerade as a legitimate client to invoke sensitive tools.

Sample Code

{
  "jsonrpc": "2.0",
  "method": "handshake",
  "params": {
    "client_version": "1.2",
    "auth_token": "<JWT_OR_OAUTH_TOKEN>"
  },
  "id": 1
}

// Server side example (pseudo-code):
if !validateToken(request.params.auth_token) {
  return { "error": "Unauthorized client" }
}

// Proceed with version negotiation only if auth succeeds

Threat 5: Tool Poisoning | Phase: Operation

A malicious actor alters or corrupts an existing tool so that when the LLM calls it, the results are tampered with or harmful.

Mitigation Plan

• Store tool executables or scripts in read-only or signed containers.
• Implement checksums or hash validations for each tool invocation.
• Use a secure registry that logs changes and triggers alerts on unauthorized edits.

Example

• An attacker replaces the legitimate “translate” script with one that inserts propaganda or leaks user input.

Sample Code

#!/usr/bin/env bash
# safe_invoke_tool.sh
TOOL_NAME="$1"
TOOL_PATH="/mcp/tools/$TOOL_NAME"
CHECKSUM_PATH="/mcp/tools/$TOOL_NAME.sha256"

# 1) Verify checksum
sha256sum -c "$CHECKSUM_PATH" || {
  echo "Checksum mismatch! Potential Tool Poisoning."
  exit 1
}

# 2) Execute the tool if safe
"$TOOL_PATH"

Threat 6: Credential Theft | Phase: Operation

• Attackers steal API keys or tokens used by the MCP client/server, gaining unauthorized access to resources or tools.

Mitigation Plan

• Use short-lived tokens with frequent rotation.
• Encrypt credentials at rest (e.g., using a secrets manager) and in transit (TLS).
• Implement multi-factor authentication (MFA) for privileged operations.

Example

• A dev environment log file contains an unencrypted token for the MCP server. An attacker finds the log on a shared drive and uses the token to invoke admin-level tools.

Sample Code

# secrets_config.yaml
auth:
  token_lifetime_minutes: 30
  rotate_tokens_on_reauth: true
  secrets_backend: "vault"
  encryption_key: "vault_key_id"

# On every login or handshake, generate a new short-lived token
# server-side pseudo-code
function generateToken(userId):
  token = createJWT(userId, expiry=30min)
  storeTokenInVault(token, userId)
  return token

Threat 7: Sandbox Escape | Phase: Operation

• The code or command environment for executing tools is compromised, allowing an attacker to break out of the sandbox and access the host system.

Mitigation Plan

• Run tools in isolated containers or VMs with minimal privileges (no root access).
• Use seccomp, AppArmor, or other kernel-level sandbox mechanisms.
• Disable unneeded system calls and network access for sandboxed processes.

Example

• A malicious or buggy “image_processing” tool triggers an OS exploit, escaping the container to read sensitive host files.

Sample Code

docker run \
  --cap-drop ALL \
  --security-opt no-new-privileges \
  --security-opt seccomp=/path/to/seccomp_profile.json \
  --read-only \
  -v /safe/input:/sandbox/input:ro \
  -v /safe/output:/sandbox/output \
  mcp_tool_image:latest

Threat 8: Remote Access Control | Phase: Operation

Unauthorized or unvalidated remote control commands are sent to the MCP server, possibly leading to full takeover or command execution.

Mitigation Plan

• Require strong authentication (mutual TLS, signed requests).
• Maintain a whitelist of allowable IP addresses or domain names.
• Implement rate-limiting and usage analytics to detect suspicious control requests.

Example

• An attacker systematically tries to guess admin commands (e.g., shutdown_server, reset_config) from a remote machine, eventually succeeding without a proper auth check.

Sample Code

# server_network.yaml
remote_access:
  allowlist:
    - "192.168.1.0/24"
    - "vpn.company.com"
    - "10.0.0.0/16"
  block_unknown: true

# Server enforces that any incoming connection not from allowlisted subnets is dropped

Threat 9: Command Injection / RCE | Phase: Operation

• Attackers craft malicious input that leads to remote code execution (RCE) on the server or the tool’s environment.

Mitigation Plan

• Use parameterized commands (no direct string concatenation).
• Strictly validate or escape all user input.
• Run with minimal privileges and read-only file system if possible.

Example

• The LLM passes a user-provided filename to a shell command: rm -rf /some/path/$(malicious code), allowing an attacker to run arbitrary commands.

Sample Code

import subprocess

def safe_invoke(command, args_list):
    # "command" must be from an allowlist of known binaries
    if command not in ["grep", "cat", "ls"]:
        raise Exception("Command not allowed")

    # Ensure each argument is sanitized
    safe_args = []
    for arg in args_list:
        # Minimal check for suspicious characters
        if ";" in arg or "&" in arg or "|" in arg:
            raise Exception("Potential injection attempt")
        safe_args.append(arg)

    # Execute as a list, not a single string
    subprocess.run([command] + safe_args, check=True)

Threat 10: Tool Redefinition | Phase: Operation

• A malicious user redefines a critical tool (same name or ID) with new parameters, effectively hijacking calls to that tool.

Mitigation Plan

• Lock existing tool definitions unless an admin role updates them.
• Compare signatures or checksums to confirm tool identity hasn’t changed.
• Maintain an audit log for every tool update or registration.

Example

• A non-admin user tries to re-register “payment_processor” tool with a new entry point that funnels data to their server.

Sample Code

{
  "jsonrpc": "2.0",
  "method": "update_tool",
  "params": {
    "tool_name": "payment_processor",
    "new_version": "2.0",
    "signature": "<SIGNATURE_OF_NEW_BINARY>"
  },
  "id": 99
}

// Pseudo-code on server:
if userRole != "admin":
  return error("Unauthorized")
if !verifyToolSignature(params.signature, tool_name):
  return error("Signature mismatch!")
// proceed with update

Please refer to next section…