WASHINGTON — The Justice Department temporarily lost track of two former terrorists who had participated in its witness protection program and until recently did not disclose the fictitious identities it created for terrorism-linked witnesses to the agency that generates watch lists, allowing some who were on the no-fly list to take commercial flights under their new names, according to a new report.

A public summary of the classified report, issued Thursday by the office of the Justice Department’s independent inspector general, Michael Horowitz, revealed that the internal watchdog raised alarms with senior department officials in early 2012 about how the witness protection program was dealing with terrorism-related witnesses, leading to an overhaul of its procedures.

In a response to the report, Armando Bonilla, a senior counsel in the office of the deputy attorney general, said that department officials agreed that terrorism-related witnesses needed greater monitoring and that changes had been put in place, including a ban on commercial flights for all participants who had a “no-fly” status under their real names.

But he also defended the use of the program for terrorism cases, saying that it had been key in securing cooperation from witnesses necessary for successful prosecutions, that no “terrorism-linked witness ever has committed a single act of terrorism after entering the program” and that an F.B.I. review of participants revealed none who posed a threat to national security.