The Good Friday incident came after a reported melee involving asylum seekers at a football field near the Manus centre.
The detention centre is situated next to the Lombrum naval base operated by the PNGDF.
The PNGDF chief of staff Raymond Numa said asylum seekers were supposed to vacate the football field at 6.00pm but that when they were required to do so, some of them refused to leave.
Numa said when a base duty officer pursued the matter further, he was assaulted by asylum seekers which led to an escalation of the confrontation.
He said rocks were allegedly thrown by asylum seekers and shots fired by members of the naval base.
The PNGDF is now investigating the cause of the incident, Numa said, adding that the situation was soon brought under control, RNZI reports.
A report by the ABC says detainees in the centre took cover after a large group of men stormed the gates of the centre about 6.30pm local time on Friday.
The detainees said Australian staff ran for cover with the asylum seekers after locking the gates.
The shooting was reportedly in response to the earlier fight between asylum seekers and Defence Force personnel from the adjacent Lombrum Naval Base.
The attack follows increasing friction between asylum seekers and locals, and many fear worse violence is yet to come.
Australia’s Department of Immigration and Border Protection said in a statement one man had been injured by a rock thrown into the centre.
“There are reports PNG military personnel discharged a weapon into the air during the incident,” the statement said. “No-one was injured.”
But detainees sent photos from within the centre showing bullets and bullet damage to their accommodation.
They said at least 100 rounds were fired during the incident.
Iranian refugee Amir Taghinia was on a bus being driven into the centre when he heard shots.
“It’s crazy, many people are in shock,” he said.
“The staff were running out of the compound like crazy, I think they were getting on a ship.”
An Iranian asylum seeker, who wished to remain anonymous, said Australian security staff were sheltering inside the complex with the detainees.
“Security staff were inside, they were hiding with us,” he said.
He said the attackers used high-powered weapons and left bullet holes in building and destroyed a light fitting.
“They were repeatedly shooting and a couple of rooms have been shot,” he said.
Asylum seekers inside the centre said they did not know if anyone had been shot.
Police on the island said reinforcements were ordered to the centre to patrol its perimeter and protect detainees, but they were not sure who the attackers were.
“We have police on the ground and they are trying to contain the situation,” Provincial Police Commander David Yapu said shortly after the reports of an incident emerged.
The incident highlights the escalating tensions on the island, where more than 800 asylum seekers and refugees remain, the ABC says.
It is not the first time there has been high-level violence at the centre.
Iranian asylum seeker Reza Barati was killed and dozens more people were injured when guards and local people responded to a protest in February 2014. - ABC/RNZI