Tapia set up a 2 November bout against Marco Antonio Barrera, instead of organising a title defence by 27 October in accordance with IBF rules.
"The IBF rules say that no champion should engage in a bout within 60 days of a mandatory defense of the title," said IBF ratings chairman Daryl Peoples.
"The 60-day rule would have been violated when he fought Barrera."
Tapia won his fifth world title belt when he beat Manuel Medina on points in New York on 27 April.
"I'm at a loss to why these guys (the Tapia camp) didn't apply for an extension, or maybe the title wasn't that important to Johnny," Peoples said.
"We have to enforce our rule."
Mike Mozes, Tapia's lawyer in Albuquerque, New Mexico, said the fighter wanted to keep the IBF crown.
"We really wanted to look at the value of that title after the Barrera fight," Mozes said.
"On the money side, we wanted to see if we could promote it, and was it a wise thing to do that."
Peoples said the IBF will schedule a fight for the featherweight title between the leading available contenders - top-ranked Juan Marquez of Mexico and Medina.
Tapia has formerly held World Boxing Organization and World Boxing Association bantamweight titles, and the IBF and WBO junior bantamweight titles.