The large group sat in 30-degree temperatures on the side of the Stuart Highway pleading for authorities to re-examine their failed bids for refugee status.
Police circled in on the group this afternoon ending the stand-off.
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Assistant Police Commissioner Rob Kendrick says he's pleased with the way the incident has been resolved peacefully.
Seventy-six asylum seekers were taken into police custody and are being held at the Darwin watch house as unlawful non-citizens while five are in the custody of immigration officials at the Royal Darwin Hospital.
Police prepared for a long standoff
Police had prepared for a long standoff with Afghan asylum seekers who staged the mass breakout.
Police struggled to convince detainees to return to the facility after they broke through security fences about 6am (CST) on Wednesday.
Officers were reluctant to use force, saying the men are engaged in a peaceful protest and hope to resolve the standoff through negotiation.
Officers earlier body-searched the men to ensure they were not armed.
The large group staged a sit-in in 30-degree temperatures on the side of the Stuart Highway, pleading for authorities to re-examine their failed bids for refugee status.
Police brought in portaloos and other equipment in preparation for a long wait.
"If I go back, they will cut off my head," one of the men, Kazemi Syed Zulfiger, told reporters.
Another, Hussaine Ali, handed reporters what he said was a threat he'd received from the Taliban saying he'd be killed if he returned home.
Five protesters have been taken to Royal Darwin Hospital, including two suffering from heat exhaustion.
Investigation underway
Meanwhile, the immigration department says an investigation is underway into how so many detainees managed to breach security measures, including two electric fences.
The federal opposition has seized on the breakout as proof that Labor's "detention network" is at breaking point because the Gillard government can't stop illegal boat arrivals.
"It's symptomatic of a detention network that's been pushed to complete breaking point. There are more than 4100 people who are now being detained ... as a result of Labor's failed policies," opposition immigration spokesman Scott Morrison said.
Wednesday's breakout is the latest in a series of problems at the centre.
On Sunday, accused Indonesian people smugglers rioted at the centre, setting mattresses on fire and, armed with poles, demonstrated on a rooftop. Some of the same protesters climbed back onto the roof on Monday.
In mid-August, the immigration department said fighting had broken out among two small groups of asylum seekers at the facility.
The Immigration Department has said it could not comment on the protesters' individual cases, other than to say all refugee claims were dealt with according to procedure and on the available evidence.
"We are managing the situation and attempting to have them moved back inside," a spokesman for the department said.
"My understanding is it's a group of about 60 or 70. It's believed they are Afghan."
Police had earlier put the number at 92.
