In addition, the U.S. Marshals Service, which handles the relocation of witnesses through the program, lost track of two former terrorists last July, a public summary of the classified report by Justice Department Inspector General Michael Horowitz said.
The public summary can be found online at tinyurl.com/Inspector-General.
The Justice Department told the inspector general's independent investigators the number of known or suspected terrorists in the program amounted to less than 1 percent of the 18,300 people who have participated in the program since its inception 42 years ago, the 17-page summary said.
It said just two individuals had been terrorists over the past six years, the report summary said.
But "we found that the department did not definitively know how many known or suspected terrorists" were admitted into the program -- and even if the number amounted less than 1 percent, that number, while small, is "significant," the report said.
One percent of 18,300 is 183.
The Witness Security Program currently has about 700 active participants. Most were involved in organized crime, violent gangs or drug trafficking, the Justice Department said.
The watchdog report found "significant deficiencies" in the department's overall handling of known or suspected terrorists admitted into the program.
Specifically, the department did not share the new identities with the FBI's Terrorist Screening Center, the report said.
That repository is used to generate other U.S. counter-terrorism databases, including the "no-fly list" maintained by the Transportation Security Administration.
"Therefore, it was possible for known or suspected terrorists to fly on commercial airplanes in or over the United States and evade one of the government's primary means of identifying and tracking terrorists' movements and actions," the report said.
In a briefing for reporters Thursday, the Justice Department declined to say how many cooperating-witness terrorists on the no-fly list actually flew under their new identities and authentic documentation.
It also said it had since fixed that problem by not letting people in the program who had no-fly status beforehand travel on commercial flights.
In a separate response, Armando Bonilla, a senior counsel to the deputy U.S. attorney general, said no "terrorism-linked witness ever has committed a single act of terrorism after entering the program."
He added an FBI review of participants revealed none posed a threat to national security.
The inspector general also said the Marshals Service said last July it was unable to locate two former witness-protection participants. With the FBI's help, it located one outside the United States and said the other was "believed" living outside the United States, the report said.
The summary provided no details about who the two people were, how long ago they had been in the program and when and why they dropped out of it.
The report -- particularly the part that said terrorists with new identities were allowed to board commercial flights in the United States -- prompted swift condemnation from Republican lawmakers.
"This is gross mismanagement -- pure and simple -- that jeopardizes American lives and cannot be tolerated," House Judiciary Committee Chairman Bob Goodlatte, R-Va., said in a statement.
"This lack of interagency information sharing appears to be systemic," he said. "We witnessed similar interagency sharing problems leading up to last month's bombings in Boston."
He said he would hold a hearing on this "outrageous problem," while Senate Judiciary Committee member Charles Grassley, R-Iowa, the ranking Republican, said the report raised "concerns" about prosecuting terrorists in civilian courts.
All but one of the inspector general's 16 recommendations have been addressed, and the Justice Department is "in the process" of carrying out the last recommendation, the report said.