The ABC has been told AFP and security officers removed six detainees from their compounds in the centre, about 80 kilometres north-east of Perth.

The Department of Immigration and Border Protection said a small number of detainees were still engaged in the protest and trained negotiators were at the scene.

It said despite this, "normal routines" were being followed at the centre.

Detainees at the facility said the protest, which began on Thursday, was sparked by unhappiness about the time it took to process their cases and cuts to after-hours medical care.

The Refugee Action Coalition's Ian Rintoul said while most detainees came down from the roof on Thursday, another 30 climbed back up last night.

"The actions of police have provoked a bigger demonstration inside Yongah Hill, and people have now gone back up on the roof to continue the protest," he said.

"What needs to happen is for the Government and Immigration to actually address the fundamental problems."

The ABC spoke to one protester who said six detainees were told they would be "transferred".

"We don't have any idea what happened to them after they took them," he said.

"We are doing a peaceful protest, we just want to be heard.

"We want to be heard by someone who is going to take our matters seriously.

"Especially people that have been detained for two or three or four years without getting progress in their cases."

The detainee, who did not want to be named, said there were about 30 people on the roof at the protest's peak, chanting and holding signs.

The department confirmed that a number of detainees had been transferred into "alternative detention arrangements" but did not say where they were being housed.

Detainees 'injured during scuffles'

Detainees at the Yongah Hill immigration centre had earlier claimed several people were injured in scuffles with guards during a protest over the level of medical care and other services provided.

 A detainee has told the ABC that one of the men who climbed up on a roof is a Lebanese detainee who had partly lost the sight in one eye after allegedly being given the wrong eye drop treatment.

Another detainee watching from the ground said a guard had told him to go back inside his accommodation unit.

"He grabbed me by my T-shirt and another officer beat me," he said.

He said he was thrown against a fence and hit his head and collapsed.

Another detainee said other men then tried to intervene and fought with guards.

Detainees used towels to mop up injured, protesters claim

He alleged several detainees were left injured and bleeding.

"Detainees were just helping each other, paper towels and bath towels were all we could use to clean up guys who were badly injured," he said.

The claims were put to the Department of Immigration and Border Protection, but it did not directly respond.

The department has also been asked if any guards were injured.

It confirmed a small number of detainees had been involved in a protest and said trained negotiators were engaging with the detainees.

But it would not comment on claims detainees were injured or whether they received medical treatment.

"It would not be appropriate to make further detailed comments on matters that are subject to continuing operations," the department said in a statement.

"The wellbeing of those in our care is a high priority for the department.

"People in immigration detention receive medical care commensurate with that available in the wider community."

The department said the centre was presently calm and normal routines were being followed.

Source: ABC News