A 41-year-old Victorian man has been charged over an incident that allegedly led to a police officer's gun "unintentionally" being fired near a cafe at Sydney Airport. 

An airline reported that a man was acting suspiciously at the T2 Terminal check-in counters, outside gate 49, about 6am today.

Australian Federal Police alleged the man became verbally and physically aggressive with two responding officers.

They allegedly tried to subdue him when a NSW Police officer and a retired NSW Police officer who were waiting to fly to Townsville, stepped in to help.

"We saw this fellow struggling with the two AFP officers. It's gone to the ground," retired officer William told 2GB.

As the man was being arrested, a federal police officer's gun was discharged and hit the wall of a nearby cafe where staff members were working.

"The AFP officer's long firearm has gone to the ground and was underneath the fellow as we went to restrain him. The shot has been discharged," William said.

"The AFP firearm was unintentionally discharged."

Images show a federal officer during the struggle moving the gun away out of reach.

Vision obtained by 2GB shows one officer sorting out the gun while others hold down the man. 

AFP Acting Commander Scott Raven told reporters this afternoon the gun had been unintentionally discharged, but refused to divulge any more details on the incident.

"The circumstances of how the firearm, which was a short-barrelled rifle, was discharged and is now subject to an internal investigation," he said.