They were there to try and remove the about 400 refugees who have refused to move to new camps at nearly Lorengau.
The police, soldiers and immigration officials entered the site early today and Mr Baki said it was a peaceful exercise with 50 inmates leaving.
He said police are doing the best they can for the refugees but they remain stubborn and defiant and are putting huge pressure on the island's community and its police resources.
However, Sudanese refugee Abdul Aziz Adam said it has been the most violent day at the centre since a deadly riot 3 years ago.
"It is really one of the scariest days and one of the terrible days that we have experienced since we came to Manus Island and everyone is really depressed and tired but people are just saying the same thing that we do not want to leave this place because we are tired of being in prison, from one prison to another prison.
"We want a pathway to a third country," he said.
Abdul Aziz Adam said no one had left voluntarily but he expected police, aided by navy personnel, who are close by, to remain at the camp overnight, putting the remaining inmates under continuous pressure to leave.
The outspoken Kurdist journalist and refugee Behrouz Boochani was taken away from the camp by police and is now at Lorengau.
Police said they did not arrest him however Mr Boochani was seen being removed in handcuffs.
He was held for about two hours, verbally abused and his belongings were destroyed.
Earlier Mr Boochani had raised concerns about at least people he said were badly hurt when the camp invasion happened.
In a final pitch to encourage what he said are the now 328 inmates left at Lombrum to leave, Police Commissioner Baki said there is now a real threat of water borne diseases developing, given water supplies and electricity had been cut off.
Photo: EMTV PNG Police Commissioner, Gary Baki.