KIRKUK, Iraq (NYTIMES) - Thousands of civilians fleeing the Iraqi military's push to evict Islamic State in Iraq and Syria (ISIS) from its last major urban stronghold in Iraq now include hundreds of suspected fighters for the extremist group, dirty and dishevelled, who arrive at checkpoints claiming innocence and begging for mercy.

While civilians from the stronghold, the city of Hawija, have sought safety in Kirkuk and elsewhere in Iraq's Kurdish region, this past weekend was the first time they came in large numbers with men of fighting age.

According to Iraqi Kurdish officials in Kirkuk, 90 per cent of these men are suspected of having been ISIS fighters - including some who may have committed beheadings and other atrocities - and they are being aggressively interrogated.

Iraqi Kurdish officials were taking no chances on Sunday (Oct 1) as they prepared one suspected fighter in a small office as his wife and four children squatted on the dirt outside.

A lieutenant in the Asayish, the Iraqi Kurdish region's intelligence service, put one hand on his holstered pistol and pointed with the other hand at a spot on the tiled floor. The prisoner understood and knelt on that spot, as an Asayish corporal tied the man's hands behind his back with a scarf.

"It doesn't matter what you do, I'm not going to spy for you," said the man, Salah Hassan, 32, who described himself as a former construction worker.

"We don't care about that," the lieutenant said. "Just tell the truth."

"Yes, tell them you're ISIS," the corporal said, brandishing a pipe in the prisoner's face. "Don't lie."

Hassan hung his head and admitted it, then looked up. "I was only a cook."

The lieutenant laughed good-naturedly. "Tens of them tell me they were cooks," he said.

"They had so many cooks, you'd think all they did was eat."

The Iraqi offensive against ISIS in Hawija began on Sept 21 and is now in its final stages, Iraqi officials say.

The army and police, backed by Shi'ite militias, are close to retaking the city, which is believed to still have 78,000 residents - and up to 3,000 ISIS fighters.

Iraqi Kurdish officials are intent on identifying any known fighters among the arriving men who may be linked to atrocities. Any with charges against them would be sent to court, while the others would eventually be allowed to rejoin their families in camps inside Iraq's Kurdish region.

The men were first stripped of their shoes, belts (which in most cases were just string or rope), turbans and any belongings, then made to kneel in rows in a large tiled room, their heads bowed forward.

Awat Jeza, an intelligence officer wearing a surgical mask and gloves, stood before 130 of the kneeling men, who had all arrived Sunday at the Asayish headquarters in Dibis, outside Kirkuk. He pulled down his mask as he told any fighters to step forward.

"Tell us who is ISIS," he said. "If you were ISIS even one minute, one hour, one day, get up now.

"Later we have lists of names and we will find out. If you are honest, you may go free. If one of you surrenders now and tells us the truth, we will be merciful with you, but if you don't, we will be -" Jeza paused, perhaps to choose the right word - "difficult."

Just in the Dibis headquarters on Sunday, there were at least 300 fighting age men, and similar numbers arrived both Saturday and Friday.

Of the Sunday arrivals, about 60 were singled out and tied up as ISIS suspects - plastic cuffs were brought in later to replace the scarves - and separated from the others. They were taken to smaller rooms, and in addition to bowing and kneeling, they were arranged so that all they could see was the wall in front of them.

Kurdish officials were anxious to show that they were not mistreating the arrivals. Major General Halo Najat Hamza, head of the Asayish intelligence service, pointed out that ISIS forces have been attacking Kirkuk from Hawija for three years. When fighters of the peshmerga, the Kurdish region's military force, have been captured, they are often tortured and beheaded.

"All night long they are shooting at us here," he said, "and now they say, 'We were all just farmers, or cooks.' And now they come to us to protect them."

A common theme in the interrogations was disavowal of many of the extremists' infamies.

Kneeling with hands bound behind his back, Gomah Salah, 58, confirmed that he had served in ISIS as a "coordinator", which he said had involved not fighting but checking resident identification cards. This made the intelligence corporal laugh.

"I swear to God, I never participated in beheadings or anything like that," Salah said. "I never even saw a beheading."

He did confirm that he had heard such things took place in Hawija.

"He's a liar," the corporal said. "We will have his name, we'll know all about him."

A few miles away, on the peshmerga front lines with ISIS positions in the Hawija area at a village called Ala Ghera, Kurdish forces on Sunday were receiving a stream of unarmed young men, with women and children. They separated the men, then had female peshmerga soldiers body-search the women in a tent.

While most of the men denied they had been ISIS fighters, most of the women routinely admitted they were from ISIS families, according to the female Kurdish soldiers.

"We are fleeing because of all the air strikes," one of the refugee women said, surrounded by four small children.

The US-led coalition has been bombing ISIS positions in Hawija intensively in support of the Iraqi offensive.

The peshmerga commander for the western zone of Kirkuk, Kamel Kirkuki, toured the front lines where refugees from Hawija were crossing and addressed 20 men who had just arrived, segregated from the others.

"Your pride, your honour, your wife and your sister will be safe here," he told them. "I promise you no one will touch you."

One of the arrivals thanked him and said, "We knew we could trust the Kurds."

When Kirkuki's delegation left, however, the men glowered sullenly at visitors.

While the peshmerga fighters have not actively joined the offensive in Hawija, their leaders expressed support for the operation, and were happy to be removing potential fighters from the battlefield.

It was strong evidence that the dispute between the Iraqi Kurds and central government over the Kurdish vote for independence on Sept 25 had not affected their military cooperation against the ISIS.

"We are supporting them in everything from our side," said Kirkuki.

The Iraqi Kurds had opened roads, shared GPS coordinates of ISIS positions and offered their hospitals for wounded Iraqi fighters.

"If they need it," he added, "they can have any help from our side."

Kirkuki said the ISIS fighters, most of them Iraqi Sunnis, are fleeing toward Kurdish lines for fear of the Shi'ite militias, which have committed extrajudicial executions, sometimes shared on social media.

Hassan, the bound suspect, agreed. "We hear they just kill us."