Music videos from artists including Madonna, Red Hot Chili Peppers and Kid Rock are among those that have started being removed.
The order could affect hundreds of thousands of video clips as it covers Warner's recorded artists, as well as the rights for songs published by its Warner/Chappell unit, which includes many artists not signed to Warner Music record labels.
Warner and had been negotiating a new licensing deal for months but talks came to a head on Friday.
The record label is disputing the fee that YouTube pays when videos are watched.
It reportedly receives less than a penny each time a video is viewed, or a percentage of the value of an ad alongside the video, whichever is greater.
Warner said in a statement: "We simply cannot accept terms that fail to appropriately and fairly compensate recording artists, songwriters, labels and publishers for the value they provide."
YouTube notified users about the removal of Warner Music content via its blog.
The blog statement said: "Despite our constant efforts, it isn't always possible to maintain their innovative agreements.
Sometimes, if we can't reach acceptable business terms, we must part ways with successful partners."
YouTube, which attracted about 100m users in the US alone during October, according to comScore, also has agreements with Universal Music, Sony Music and EMI Music.
Warner is expected to continue distributing its music videos with other websites it has licensing agreements with, such as and .
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