It was taken down after Twitter requested its removal.
Separately, Mr Musk has told Twitter workers that the firm is worth less than half of the $44 billion 36 billion he paid for it last year.
GitHub does not usually comment on decisions to remove content. A GitHub spokesman said that in the interest of transparency, we share every DMCA Digital Millennium Copyright Act takedown request publicly.
The DMCA was signed into law in the US in 1998. It is aimed at protecting copyrighted material on the internet.
In the takedown request, Twitter asked for information on who was behind the code that was named FreeSpeechEnthusiast.
San Francisco-based Twitter said in the filing that the account had infringed copyrights owned by the company.
The leak creates a new challenge for Mr Musk, who has slashed Twitter's workforce by more than a third and faced an exodus of advertisers since buying the platform in October last year.
The Tesla chief executive has reportedly indicated that Twitter is now valued at less than $20 billion.
According to Platformer and the Information, the estimate of the company's value was based on Mr Musk's offer of stock grants to staff.
Musk told staff: I see a clear, but difficult path to a $250 B valuation, which suggests a more than tenfold increase in Twitter's valuation.
The press office email account automatically responded to a poo emoji, an approach that Mr Musk announced earlier this month, in response to a BBC request for comment.