Three months after Florida police shot and killed a computer engineer walking with an unloaded air rifle, two of the officers involved received awards for bravery, even though the incident was still under investigation.

Now their boss — who stood next to them at the ceremony — says those commendations were a mistake and plans to revise department rules.

"The policy was violated," Broward County Sheriff Scott Israel told NBC News. "They should not have received the awards."

Israel said he was not involved in the awards process until the evening of the semi-annual ceremony and he doesn't know who signed off on the awards — because the paperwork was accidentally destroyed.

Gold Cross Award winners, from left, Sgt. Richard LaCerra and Deputy Peter Peraza stand with Sheriff Scott Israel during the Broward Sheriff’s Office Awards Ceremony at the African-American Research Library in Fort Lauderdale in 2013. Amy Beth Bennett / Sun Sentinel

The awards stemmed from the shooting of Jermaine McBean as he walked home from a pawn shop on July 31, 2013. Police say that after three people called 911 in alarm to report a man with a gun, McBean ignored their shouts to drop the weapon and pointed it at them, giving them no choice but to fire.

Questions about the police account have been raised by a witness to the shooting and a photo of the dead man that seems to show him with earbuds in his ears. Prosecutors have not yet handed over the case to a grand jury, and the FBI is keeping tabs on it.

READ: NBC News' original report on the death of Jermaine McBean

While the investigation has dragged on for more than two years, the decision to give the officers awards was swift. Deputy Peter Peraza, who filed the fatal shots, and Sgt. Richard LaCerra were nominated by a lieutenant a month after McBean's death.

His memo lauded Peraza and LaCerra for "selfless, honorable and brave" actions in the face of a suspect waving a rifle in a "threatening manner." It did not mention that the weapon in question was later found to be an unloaded air rifle.

The sheriff's office said Israel did not know Peraza and LaCerra would be commended until he showed up to present a raft of awards at the African-American Research Library and Cultural Center in Fort Lauderdale on Oct. 22, 2013.

But it wasn't until McBean's family filed a lawsuit last spring, alleging the award was part of a wrongful-death coverup, that Israel ordered an Internal Affairs review of the combat cross rewards.

That probe found that the deputy in charge of coordinating the awards had shredded the applications that would have contained approval signatures up the chain of command.

"There was no malice," Israel said of the shredding.

The Internal Affairs report, filed in late August and obtained through a public-records request, says the deputy had destroyed all completed awards when another officer took over the coordinator position — even though such records must be kept for five years under state law.

The deputy who got rid of the material "was unaware that she was supposed to retain the forms and was apologetic for her actions," the report says. She received a written reprimand.

Regardless of what was in the missing material, the award violated the sheriff's policies, which said that if the nominee fired a gun, the findings of the Shooting Review Board must be included in the application and considered.

Israel said it appears that was not done. He has now proposed a revised policy that says an officer who kills someone cannot be given an award until all criminal and administrative reviews are complete unless "specifically authorized by the Sheriff."

Jermaine McBean with an alligator Courtesy Davod Schoen

"These awards could have been given at any time," he said of the commendations for the McBean shooting. "There should not be a rush to give awards."

Israel said he will not rescind the awards because the Broward State Attorney's office could soon be presenting the case to a grand jury and any action he takes could influence the outcome.

"Now is not the time to do that," he said.

David Schoen, a lawyer for McBean's family, said they were "deeply saddened" to hear the sheriff won't recall the awards.

"It has been a terrible slap in the face to the McBean family from the day it was given," he said.

"This award is alleged to be a part of that coverup and allowing it to remain in place just further supports that assertion."

Activists from the Black Lives Matter movement have also called on the sheriff to rescind the award and remove the three officers involved in McBean's death from the street.

"Scott Israel obviously is trying to influence the outcome. In favor of his officers!" said Jeff Weinberger, an organizer with the Black Lives Matter Alliance in Broward. "If he acknowledges that the awards shouldn't have been given, then why not rescind them?"

McBean's family says a photo taken by a witness shows that the police lied about the circumstances of his death. In the picture, he appears to be wearing white earbuds — even though police insisted he had nothing in his ears that would have stopped him from hearing their shouts and told the family the earbuds were found in his pants pocket.

One witness has also told NBC News that McBean was holding the air rifle — which he had just bought — behind his neck as he walked into his Oakland Park apartment complex and never pointed it at the officers responding to the 911 calls.

Israel has said there was "no coverup" by his department. In court papers, a lawyer for the department and the officers says McBean's actions were to blame for his death.