The animal rights organisation has said the Nintendo mascot's use of a Tanooki suit sends a wrong message about wearing animal fur.
PETA has also created a flash game on its website, where players control a skinless tanuki that chases a flying Mario through a stage.
"When on a mission to rescue the princess, Mario has been known to use any means necessary to defeat his enemy - even wearing the skin of a raccoon dog to give him special powers," read a statement from the firm.
"Tanooki may be just a 'suit' in Mario games, but in real life, tanuki are raccoon dogs who are skinned alive for their fur. By wearing Tanooki, Mario is sending the message that it's okay to wear fur. Play Super Tanooki Skin 2D and help Tanooki reclaim his fur!"
Last year, PETA told Digital Spy that it was "pleased" Super Meat Boy included its spoof character Super Tofu Boy in the PC version of the game.
Super Mario 3D Land is out now in North America and on November 18 in Europe.