The Mouse House is turning its back on the Annie Awards.

Hollywood’s longest running toon kudofest, which Disney has sponsored since its first year in 1972, will have to go on without submissions or support from Walt Disney and Pixar Animation Studios.

“After more than a year of discussions with the ASIFA board, we have regretfully decided to withdraw from the organization and no longer participate in the annual Annie Awards,” said Disney-Pixar prexy Ed Catmull.

“We believe there is an issue with the way the Annies are judged, and have been seeking a mutually agreeable solution with the board. Although some initial steps have been taken, the board informed us that no further changes would be made to address our concerns.”

While some at Disney suggested the move could cripple ASIFA-Hollywood — a 5,000-strong organization of animation professionals and enthusiasts — by rendering its top prize “the best animated feature not produced by Disney-Pixar,” org chief Antran Manoogian insisted releases such as Pixar’s “Toy Story 3” and Disney Animation’s “Tangled” can still compete.

Catmull’s criticisms come at a time when animated features have been driving the box office, boosted by the use of 3D in the field. Though the Annies predate the addition of animated feature categories to such award shows as the Oscars, Golden Globes and the PGA Awards, the rise of such prestigious competition has forced ASIFA to reevaluate its own process in order to remain credible.

“The Annies have become recognized as the animation community’s award,” Manoogian said. “In maintaining that standard, the board members felt it was important that we make this an industry prize where only qualified animation professionals working in a creative capacity get to determine that award.”

At issue was the fact that anyone can buy a membership to ASIFA (not unlike Film Independent, whose paying members vote for the Spirit Awards), whereas members of the Motion Picture Academy and other awards-giving bodies must be voted in by their peers.

Some, including those in the Disney camp, have charged that the distribution is tilted in favor of DreamWorks Animation, which gives each new employee an ASIFA membership upon joining the company. While that hasn’t prevented Pixar toons from winning six of the past 10 Annie feature awards, “Wall-E’s” 2009 shutout caught many by surprise, with “Kung Fu Panda” taking the top prize that year.

In response to Disney pressures, ASIFA tightened its rules somewhat last year, limiting the voting on individual achievement categories to animation pros (students and non-professionals were still permitted to vote in production categories, such as best animated feature).

Manoogian refers to those changes as a “midstep” toward this year’s dramatic overhaul, which requires all members wishing to vote in the Annie awards to be approved by a qualifying committee. Non-pros will not be able to vote in any category.

That wasn’t enough for Catmull, who had called for an advisory committee of toon execs representing each studio to recommend rule changes to the ASIFA board. In an email sent to Disney-Pixar employees stating the company’s position, Catmull wrote, “Individuals are encouraged to maintain their memberships and support for the Annies as they deem appropriate.”

So, while the Mouse House will not be submitting the names of its most deserving below-the-line talent for Annie consideration, as other studios do, Disney-Pixar producers and artists may still enter their own work by ASIFA’s Oct. 15 deadline. Even if individual artists fail to submit, Manoogian expects Disney-Pixar to be well represented on future ballots.

“The Annies are about honoring the best in animation, and we will continue to do so,” he said. “The awards are set up in such a way that the nominating committee can put a nominee on the ballot even though it hasn’t been formally submitted.”