The company said it had shut down internal processing systems in order to ensure that data did not get corrupted.
The site's status page indicates that the recovery process is still going on, nearly 24 hours after initial reports of the service being affected.
Microsoft paid US$7.5 billion (A$9.79 billion) in its own stock for GitHub in June and the deal was given the green light by the European Union on 19 October.
The statement about the borking of the site said: "We are aware of how important our services are to your development workflows and are actively working to establish an estimated timeframe for full recovery.
"We will share this information with you as soon as it is available. During this time, information displayed on GitHub.com is likely to appear out of date; however no data was lost.
"Once service is fully restored, everything should appear as expected. Further, this incident only impacted website metadata stored in our MySQL databases, such as issues and pull requests. Git repository data remains unaffected and has been available throughout the incident."