Rovo MCP Server only returns Teamwork Graph tools when using API Token

Summary

When integrating the Atlassian Rovo Model Context Protocol (MCP) server (e.g., with GitHub Copilot or other AI agents) using an Atlassian API token, the tools/list call only returns a limited set of tools (typically 2-3 Teamwork Graph tools like getTeamworkGraphContext and getTeamworkGraphObject).

Diagnosis

Expected tools for Jira and Confluence (such as getJiraIssue, searchJiraIssuesUsingJql, getConfluencePage, etc.) are missing from the list, even though the service account has the necessary product access.

Cause

This behavior is due to scope-based filtering at the authentication layer. The Rovo MCP server dynamically filters the available tools based on the scopes present in the provided credential.

Common reasons for missing tools include:

1. Legacy API Tokens: Using a legacy API token that does not support granular scopes.

2. Classic Scopes: Using broad "classic" scopes (e.g., read:confluence-content.all) which are not recognized by the MCP server.

3. Incorrect Auth Format: Sending the token as a raw Bearer token instead of the required Basic encoding.

Solution

To resolve this, you must generate a modern, scoped API token and ensure it is sent with the correct encoding and granular scopes.

1. Generate a Scoped API Token

Create a new API token for the service account and ensure the following granular scopes are explicitly selected:

• Jira: read:jira-work

• Confluence: read:page:confluence and search:confluence

• Rovo: search:rovo:mcp

Note: Broad scopes like read:confluence-content.all will not work for MCP tool discovery.

2. Use Basic Authentication

The Atlassian MCP server requires Basic Authentication. The token must be encoded as follows:

• Header: Authorization: Basic <base64(email:api_token)>

• Do not use Authorization: Bearer <api_token>.

3. Verify the Configuration

After updating the token, restart your MCP client and call tools/list. The response should now include the full suite of Jira and Confluence tools.

Troubleshooting

If the tools are still missing after following the steps above:

1. Check Response Headers: Look for the Atl-Traceid in the HTTP response headers.

2. Contact Support: Provide the Atl-Traceid and the specific list of scopes you have configured so that Atlassian engineering can inspect the server-side logs to see why the scopes are not being recognized.