August 17, 2013 - 18:03 AMT
The two companies had collaborated on a HTML5 application, but the web giant claims that the Redmond company has failed to make the necessary browser upgrades.
"Microsoft has not made the browser upgrades necessary to enable a fully-featured YouTube experience, and has instead re-released a YouTube app that violates our Terms of Service," a Google spokesperson told The Verge.
"It has been disabled. We value our broad developer community and therefore ask everyone to adhere to the same guidelines."
Microsoft has hit out at Google's reasons for pulling the Windows Phone YouTube app, calling them "manufactured".
"It seems to us that Google's reasons for blocking our app are manufactured so that we can't give our users the same experience Android and iPhone users are getting," said Microsoft deputy general counsel David Howard in a blog post.
"The roadblocks Google has set up are impossible to overcome, and they know it."
The two parties are believed to be working together on a solution.