YouTube has given Microsoft a week to remove an app from its Windows Phone store.
The Google-owned company claims the app blocks adverts and allows users to download videos.
In a letter obtained by Wired.com YouTube claims the app's features "harm our content creators and clearly violate our Terms of Service".
A statement issued by Microsoft in response says the company "look forward to solving the matter".
Microsoft built the app after claiming Google refused to help develop a native Windows Phone app.
The app also allows users to play videos that creators had blocked from mobile devices.
YouTube's Director of Global Platform Partnerships Francisco Varela has requested the app is withdrawn by 22 May.
MicrosoftIn light of (Google CEO) Larry Page's comments today calling for more interoperability and less negativity, we look forward to solving this matter together for our mutual customers
The letter addressed to Todd Brix, General Manager of Windows Phone Apps and Store, says the company were "surprised and disappointed".
It accuses Microsoft of launching an application that "deliberately deprives content creators of their rightful earnings".
YouTube points out that Windows Phone 8 are able to use a "fully-functional" YouTube application through the web browser.
The letter suggests Microsoft's app "cuts off a valuable ongoing revenue source for creators, and causes harm to the thriving content ecosystem on YouTube".
In January 2013 Microsoft Vice President Dave Heiner said "Google blocked Microsoft's new Windows Phones from operating properly with YouTube".
Microsoft claims Google refused to help develop a native YouTube app for Windows Phone
Microsoft has said the response to its app has been "overwhelmingly positive".
The company says it would be "more than happy to include advertising" but needs Google to co-operate.
In reference to Google CEO Larry Page's comments at Google's I/O developers conference, Microsoft says it looks forward to finding a solution.
"In light of Larry Page's comments today calling for more interoperability and less negativity, we look forward to solving this matter together for our mutual customers." the company said.
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