Organizers of the popular Five Boro Bike Tour wants the NYPD to scrap a new, $1 million fee for traffic control during the annual ride, according to a lawsuit filed in Manhattan civil court.

Advocacy group Bike New York, which runs the tour, says the cost would cripple the nonprofit and threaten free classes planned for the upcoming Bike Share program.

Group director Kenneth Podziba claims imposing the fee for the first time after 35 years is unfair.

The city imposed the fee in March, saying the 40-mile ride — on May 5 — is a “noncharitable athletic parade” because its 32,000 participants are charged $86 to enter.