Police surrounded 92 detainees on the side of the Stuart Highway on the outskirts of Darwin.

Some of the men were carrying messages written on sheets declaring "we want protection" and "show us mercy".

The men have all applied for refugee status. One man told reporters most of them have had their claims rejected and immigration officials have told them they will have to return to Afghanistan.

A man yelled to reporters that if they have to return to Afghanistan they would be killed.

He said: "If Afghanistan is safe, why are there Australian soldiers there? Why are there American soldiers there?"

Police prevented the detainees from handing notes to reporters.

The detainees broke out through two high-wire fences that surround the centre in the grounds of the Coonawarra Naval Base about 7am.

A police officer said it was not believed any detainees escaped into the Darwin community.

"They are sitting down peacefully to make their views known," the officer said.

An Immigration Department spokesman said "all the detainees are accounted for".

A police negotiator told the detainees that police would be far more relaxed if they were allowed to search them.

The detainees agreed and resumed their position by the side of the road, holding their banners after the process.

"I am so thankful for you behaving peacefully," a police negotiator told them. "I am trying to get something sorted out for you," he said.

At 11am - four hours after the protest started - the detainees remained sitting in the open in 30-degree-plus heat, without shade and with only a few water bottles. Some of the men might be fasting as part of the holy Islamic month of Ramadan.

Sandy Logan of the Department of Immigration told Sky News the detainees were being "very co-operative" and his department's only concern was about the impact on traffic.

He said the matter was "under control" and NT police were returning the detainees to the detention centre.

The breakout raises concerns about security at the centre, which holds almost 500 detainees.

Indonesian detainees protest

Teams of Northern Territory, Federal Police and security guards have failed to restore calm among 151 Indonesian detainees in the centre since Sunday, when a dozen men brandishing poles and yelling abuse climbed on to the roof of demountables at the centre.

The men also set fire to rubbish and mattresses, sending a plume of back smoke across the outskirts of Darwin.

The Indonesian detainees are protesting against their legal treatment, which includes delays of up to nine months in having their cases come to court.

Immigration officials have attempted to play down the protests and have released only scant details about them.

At least one guard suffered minor injuries and government property has been damaged.

Lindsay Murdoch is Fairfax Media's Darwin Correspondent.

- with Glenda Kwek