The war of words took place at the end of the two-hour meeting at Antun’s in Queens Village when union delegates from the Patrolmen's Benevolent Association began shouting at Lynch, demanding to know what came out of a recent meeting with the mayor, a law-enforcement source said.
Lynch replied that the unions made no headway with the mayor.
When Dets. Rafael Ramos and Wenjian Liu were murdered last month in Brooklyn, Lynch said that de Blasio had "blood on his hands."
The officers at the union meeting also wanted answers from Lynch about getting heavier weapons, better bulletproof vests and new patrol cars, the source said.
Liu and Ramos were sitting in their patrol cars when gunman Ismaaiyl Brinsley opened fire, killing them, sparking a call for greater protections for officers.
According to sources, the officers who spoke out against Lynch are believed to be aligned with a small Bronx-based faction of delegates considering running against Lynch this year.
Lynch downplayed the clash and continued to point the finger at elected officials.
“A few agitators bent on their own selfish agendas were simply attempting to use legitimate complaints about City Hall to try to repair their own weakened and damaged credibility,” Lynch said in a statement.
“We will continue to voice the serious concerns of New York City police officers to this administration at City Hall and Police Plaza and not be distracted by side shows.”
In an unrelated press conference in The Bronx Wednesday, de Blasio said he wasn't surprised at the diversity of opinion within the ranks of the NYPD.
"I've separated a long time ago some of the specific things some of the union leaders have said from what is felt by the rank and file. This wouldn't be the first case where that is true," de Blasio said in response to a question about the meeting.
The mayor also said there would be no apology. "You can't apologize for your fundamental beliefs. I think they have been warped and misinterpreted many times over," said de Blasio.
Instead, the mayor said more attention should be paid to addressing the concerns of rank and file officers regarding safety and equipment.
"We have to focus on officer safety as part of the package of reforms we are making in the city to make everyone safer," the mayor said.
Jeff Mays contributed reporting.