The allegations stem from a 2015 incident involving Isa Hackett Dick, executive producer of Amazon's "The Man In The High Castle" and upcoming "Electric Dreams", according to The Hollywood Reporter.
"Roy Price is on leave of absence effective immediately," an Amazon spokesperson said in a statement.
Amazon said the studio's COO Albert Cheng will take over the division on an interim basis.
The statement also said that the company was reviewing options for their projects with The Weinstein Co.
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The producer said she reported the incident immediately to Amazon executives. An outside investigator was brought in to speak to Hackett as well as the Amazon executives.
Hackett said Price, who is also the global head of Prime Video content, did not appear at any events involving her shows thereafter.
Amazon is also reviewing the two shows from the Weinstein Co Matthew Weiner's "The Romanoffs" and director David O Russell's untitled drama
in the wake of rape and sexual harassment allegations against former co-founder Harvey Weinstein.
"@JeffBezos I told the head of your studio that HW raped me. Over & over I said it. He said it hadn't been proven. I said I was the proof," she tweeted, identifying Weinstein as the assailant for the first time.
McGowan spoke last year about being raped by an unnamed studio head, but did not name Weinstein. The producer reached a settlement with McGowan when she was 23, after "an episode in a hotel room" during a film festival, according to the New York Times expose on Weinstein.