Search API not returning all results for internal repositories

I am using an OAuth token to search for repositories using Search API. For my own personal token, I get complete search results for internal repositories matching the query, and on the other hand, for the OAuth token with the same permissions (scopes), it only returns a subset of internal repositories for the same query.

If we add the org name in the query, the API returns the repository that wasn’t showing up before so it’s not something about visibility and accessibility of the owner of the token to the repository.

Any idea on why it’s returning different results?