Lawyers for the city asked a judge Thursday to find the merchants in contempt of court.
The development is the latest in a legal battle between Mayor Michael Bloomberg and smoke shops on the Poospatuck Indian Reservation.
A federal judge declared in August that the shops’ multimillion dollar business in untaxed cigarettes was illegal and had to stop.
Tribal representatives say the stores obeyed the order and shut down.
But the city says at least three owners are still secretly doing business.
The tribe’s chief says the allegation isn’t true.