Moore's lawsuit, which was filed Monday in Los Angeles Superior Court, claims the filmmaker is owed at least $2.7 million for the 2004 documentary.
According to the lawsuit, the Weinsteins, who distributed "Fahrenheit 9/11," agreed to pay Moore half of the film's profits. However, an audit showed several accounting irregularities that cut into the filmmaker's payments.
The film, which centered on the Bush White House's actions after the Sept. 11 attacks, grossed more than $100 million.
The Weinsteins' attorney, Bert Fields, said Moore's lawsuit should be thrown out.
"Michael Moore has been paid $20 million and he claims he should get $2 million more," Fields said Tuesday. "His claims are hogwash. They are totally without merit. He's been paid every dime he's entitled to."
Moore is known for his Academy Award-winning documentary, "Bowling for Columbine," which looked at gun control in the United States, and his latest project was titled, "Capitalism: A Love Story."
The Associated Press contributed to this report.
