The escapees enjoyed a short-lived freedom and "within about an hour and a quarter, control was restored to the center," he said
Australian Broadcasting Corp. reported Morrison saying the breakout happened about 6:15 p.m. local time and was the result of "much-heightened" tensions at the facility.
Disturbances began after immigration officials told asylum seekers if they weren't bona fide refugees, they wouldn't be settled in Australia or Papua New Guinea, which owns Manus Island.
"It is our intention they will never be resettled in Australia," Morrison said in a press conference in Canberra.
Asylum seekers reportedly tried to shatter windows, threw tents over the perimeter fence and used parts of smashed bunk beds as weapons, before 35 detainees fled the compound.
The disturbance is the latest controversy to hit the detention camp, home to around 1,300 people.
Australia's navy has picked up the majority of detainees, found adrift on the high seas after paying people smugglers for an attempted passage to Australia.
Refugee and human rights groups including Amnesty International have criticized the camp for its poor living conditions.
The Sydney Morning Herald reported Labor party immigration spokesman Richard Marles said the government must ensure riots such as this week's event don't happen again.
"This is now the second serious incident which has occurred at the Manus Island detention facility since the [Liberal party] Abbott government came to power," Marles said.
During the first security incident at Manus, in October, Manus detainees accused Australian officials of abandoning them when a violent brawl erupted between rival Papuan security forces.
The West Australian newspaper reported Royal PNG Constabulary officers clashed with PNG Defense personnel outside center's perimeter Oct. 18.
The West Australian reported armed PNG police were pushed and shoved by members of the PNG Defense Force carrying rocks and sticks.
Detention center personnel, including from Australia's Immigration Department, the Salvation Army, security firm G4S and contractor International Health & Medical Services, were moved into a secure area of the compound in case an evacuation was ordered.
Successive Australian governments have been criticized for the policy of maintaining offshore detention and processing centers for asylum seekers.
Amid heavy criticism from Australian human rights campaigners, the Australian government closed the Manus center, as well as one on Nauru, in 2008 after operating them for around six years.
But Australia signed an agreement with Papua New Guinea in 2012 to re-open the center on Manus, a rugged jungle-covered island measuring 60 miles by 19 miles off Papua's northern coast.
Australia also reopened a center on Nauru, an almost circular island in the South Pacific with a population of about 9,000. Nauru is under the protection of Australia, although it has been independent since 1968.
Riots broke out at the Nauru center in July after a similar announcement that detainees wouldn't be settled in Australia.
Police on Nauru captured the 59 escapees, but one policeman was stabbed and briefly held hostage during the riot, the Sydney Morning Herald reported at the time.
Amnesty International published a report on Manus in December, decrying conditions at the center as "shameful."
Amnesty said asylum seekers are being held in a "prison-like regime," in extremely cramped compounds in stifling heat with insufficient water and medical treatment.
"This system of harsh conditions and humiliating treatment is a deliberate effort to pressure people to return to the desperate situations they have fled from," Amnesty International Australia's National Director Claire Mallinson said.
"Australia is directly responsible for this deplorable and unlawful combination of arbitrary detention and inhumane conditions." she said.