It's yet to be determined whether the 81 men will be charged.
About 80 officers from the NT Police and AFP Assistant Commissioner moved in on the men before searching them and putting them in police vans.
The men have been taken to the Darwin watchhouse, which has been specially converted into an authorised detention centre following the stand off.
Assistant Commissioner Rob Kendrick said police "extremely happy" with the outcome, adding that no one was hurt.
"All came along peacefully and were compliant," Mr Kendrick said.
It's yet to determined whether the men will be charged, he said.
"They are now being held as unlawful non-citizens pursuant to the migration act. A decision will made by the immigration department as to what happens next."
Mr Kendrick would not comment on whether the group's demands had changed throughout the day.
He declined to expand on why the men were denied more access to the media.
"These persons who should be in custody have had a lot of access to the media."
Immigration Minister Chris Evans warned earlier that the asylum-seekers could be charged and private contractor Serco, which is responsible for security at the centre, could be fined.
In a media conference this afternoon Senator Evans confirmed that 92 Afghan men had pushed down a fence and moved outside the centre to hold a protest, with four being taken to hospital.
He said the situation in Darwin was "calm" and "under control" and he was in contact with the NT Chief Minister.
But earlier, police scuffled with journalists after the protesters threw a bottle containing a message about their plight.
Journalists refused to hand back the bottle, which contained five pieces of torn paper.
The hard-to-read letter made a plea for mercy from life under the Taliban. "Even the foreign forces are helpless and not safe in Afghanistan," it said.
Immigration Department spokesman Sandi Logan earlier said the men had broken through two electrified fences - an interior fence and a perimeter fence, both carrying 11,000 volts - at about 6.30 this morning.
One of the men taken to hospital was suffering from a pre-existing fit injury, another was suffering chest pains and two were suffering heat exhaustion.
Mr Logan said the men were not offered food, water or sunscreen. "It's part of the negotiating strategy," Mr Logan said.
As temperatures hit the mid 30Cs, the men took turns to hold up the eight banners they brought with them over the perimeter fence.
Many of the men have towels and appear to have a little water, but it is understood that they are fasting for the holy month of Ramadan.
Senator Evans said many of the men in the protest had had their initial asylum claim refused.
He emphasised that escaping from detention and damaging detention property was a criminal offence.
"It's a peaceful protest and most of the protest seems to be focused on supporting their asylum claim. As I understand they're all accounted for," he said.
"Serco are responsible as the private provider for the security of the detention centre and under the contract we can fine them for failure to perform to acceptable standards.
"I would say though that obviously they are under a lot of pressure given the numbers in detention currently."
Mr Evans said that if the Opposition tried to reinstate Temporary Protection Visas it would require parliament to consider new regulations that could be disallowed.
Opposition immigration spokesman Scott Morrison told The Australian Online that he was set to get a briefing from the department at 5pm today on the Darwin breach.
Today's breakout came as another boat carrying 87 asylum-seekers reached Christmas Island.
It was the sixth boat arrival in the past four days, bringing the number of arrivals to 250 arrivals since Saturday night.