GitHub MCP Server Error – SystemError in Copilot Orchestration

Question

Hello Microsoft Q&A,

I'm encountering issues with the GitHub MCP Server integration in Copilot Orchestration. When attempting to search for the a script in my private repository, I received the following error:

Code

Sorry, something went wrong. Error code: SystemError. Conversation ID: 834b82c5-df0b-4644-b5c6-bd97522072c1. Time (UTC): 1/19/2026 2:43:40 AM.

The GitHub MCP Server is configured with the following details:

• MCP tool name: GitHub MCP Server
• Connection status: connected

Available to: Agent

Credentials: Maker-provided credentials

Could you please help investigate why this error occurred and how to resolve it?

Thank you!

Answer 1

The error you are encountering, "SystemError," during the GitHub MCP Server integration in Copilot Orchestration can be attributed to several potential issues. Here are some steps you can take to troubleshoot and resolve the problem:

1. Verify GitHub App Installation: Ensure that the GitHub app is correctly installed in your organization. If it's not installed, you may encounter authentication issues.
2. Check Permissions: Make sure that the GitHub app has all the required permissions to access the private repository. Missing permissions can lead to errors when trying to perform actions like searching for scripts.
3. Credentials Verification: Since you are using maker-provided credentials, double-check that these credentials are valid and have not expired. Invalid credentials can lead to authentication failures.
4. Connection Status: Although your connection status shows as "connected," it may be worth disconnecting and reconnecting the GitHub MCP Server to refresh the connection.
5. IP Restrictions: If there are any IP restrictions in place, ensure that the IP address of the machine making the request is allowed to access the GitHub resources.
6. Consult Logs: If possible, check the logs for more detailed error messages that could provide additional context on the issue.

If these steps do not resolve the issue, consider reaching out to Microsoft support for further assistance with the specific error code and conversation ID you provided.