Runway construction at Kennedy Airport is no excuse for parking passengers on the tarmac for longer than three hours, federal officials said yesterday.

JetBlue, American and Delta — Kennedy’s three biggest airlines — all lost their requests to be exempted from the feds’ new tarmac rule while JFK’s main runway is rebuilt. The runway is slated to reopen by June 1.

The rule, which takes effect next Thursday, imposes fines of up to $27,500 per passenger when flights are held away from runways or terminals for longer than three hours.

“This is an important consumer protection, and we believe it should take effect as planned,” said US Transportation Secretary Ray LaHood.

Despite griping, airlines said they’d go along with the rule.