In a post on the site formerly known as Twitter, the bloc's industry chief said "violent and terrorist content" had not been taken down, despite warnings - as is required by EU law.
Mr Musk said his company had taken action, including by removing newly-created Hamas-affiliated accounts.
Ednews informs referring to BBC, Thierry Breton, Commissioner for the Internal Market of the European Union, did not give details on the disinformation he was referring to in his letter to Mr Musk.
However, he said that instances of "fake and manipulated images and facts" were widely reported on the social media platform.