When Sami Habib woke up early to the sound of distant gunfire in the village of al-Bashier near Kirkuk, he was not unduly alarmed. Fighters from the Islamic State of Iraq and the Levant (Isis) had carried out hit-and-run attacks before and he thought the army would repel the militants as they had done previously.

But a few hours later he was told to leave immediately as the rebels had overrun the village.

"I hurried to my Iranian wife and four children and told them to prepare themselves to leave in my little pickup with our neighbour's family. I gave the key to my eldest son, Samer, who is only 13, and told him to wait for me just outside of the village," he told the Guardian.

That was last week. Habib has not seen his family since.

"As the gunfire grew more intense, I tried to ring my son to make sure that he was alright with the family," said Habib. "My neighbour's son picked up the mobile to say that my son was shot in the leg as they came under heavy fire. I ran with my neighbour to find out about our families, we could see a few bodies scattered in the streets. As we reached the place where other villages were gathering, I asked repeatedly if anyone had seen a pickup with two families. I could not get any answer."

A few days later, Habib's sister identified the bodies of his two daughters who had fled among the 15 people killed in the village by Isis. Eighteen-year-old Sara had been killed by a bullet that went through her chest and left a hole in her back and Noor, 12, had been shot in the side.

"I was in great pain when my two young daughters were taken by Isis fighters," he said. "I could not rest for a moment not knowing their fate. I know now that I have their bodies. It's hard, but it gives me some sense of relief that I could find and bury them."

Habib's big worry now is his wife and his two sons, Samer and Ali, 4, who are still missing.

The tragedy that engulfed Habib is being repeated across Iraq as the country threatens to break apart – with Kurds preparing to go their own way – under the onslaught of Isis backed by Sunni tribes in the north. Nouri al-Maliki, the Shia prime minister, stands accused of pursuing sectarian policies that have allowed Isis to exploit Iraq's traditional Shia-Sunni divide. Maliki is being urged by the US and others to step down for a less divisive figure, but he has brushed aside calls for a government of "national salvation". As Maliki digs in his heels, the prospect of civil war looms. The human cost is already high.

Human Rights Watch on Friday said Isis killed between 160 and 190 men in at least two locations earlier this month when they captured Tikrit, the northern city and birthplace of Saddam Hussein, the former dictator.

"The photos and satellite images from Tikrit provide strong evidence of a horrible war crime that needs further investigation," said Peter Bouckaert, emergencies director at Human Rights Watch.

But atrocities are also being carried out by Shia militias, who have been summoned by the highest Shia authority in the land, Ayatollah Ali al-Sistani, to defend Shia holy shrines. The old Mahdi army, rebranded as Peace Brigades, can be counted on to stand and fight the insurgents, unlike the military. But their zeal is feared by those they target.

Hani Sa'aeed, 24, disappeared three days ago when he went to a shopping centre with a friend in Mahmoudiya, a town south of Baghdad. "After a few hours, his friend contacted us to say that Hani was taken by the Righteous League militia who are in control of the town," said Ibrahim Abdul Majid, Hani's cousin.

"The militia were so furious after four explosions rocked the centre of the city during the day and killed many people. They were busy picking up young men based on their IDs. Hani's friend advised us to act quickly to save him but we did not know what to do."

Adbul Majid eventually rang the police, who said they had found the body of a young man in a compound near the shopping centre.

"It was difficult to go to the hospital to find out if Hani was dead or still alive, the militias were everywhere," said Abdul Majid, who rang a friend at the hospital who confirmed that Hani's body was there.

"We were all scared to approach the hospital for fear of being kidnapped, we had to pay $500 for a Shia man to get the body from the hospital, he was the only one who could bring Hani's body home. When we took Hani's body to bury him, his body was full of bruises, he was killed with shots to his head, chest and leg."

Three weeks ago, Mustafa al-Douri and his cousin were kidnapped and killed by Shia militia in the city of Samara even though his mother managed to raise $100,000 in ransom money to pay for their release. When she went to get them, the kidnappers took the money and told her to wait.

"Mustafa's mother kept waiting for hours, neither her son nor his cousin showed up," Basil Walid, Mustafa's cousin, told the Guardian. "The second day, we decided to go to the fornesic department to look for Mustafa and Ammar. After checking a few bodies, we found them. They were killed only 24 hours before, according to the doctor who issued their death certificates. They were both handcuffed. Their toenails were gouged and they were shot several times in the head, chest and leg."

The victims of this conflict cross sectarian lines. Umaya Jibara, a law graduate and a mother of four, was Sunni but died while fighting Isis near al-A'alam district, 16km from Tikrit. Isis fighters had demanded the surrender of Umaya's uncle, Jassim Jibara, who is the director of national security in Tikrit, and her brother, a leader of the US-backed Sunni Awakening councils that had fought al-Qaida in 2006. Her husband took their children to Irbil while she stayed behind, vowing to defend her family.

"She was having breakfast in her eldest brother's house when suddenly gunfire erupted, the area turned into a battlefield," said Ali Kamel, her cousin. "Isis fighters were advancing through the al-A'alam groves by the Tigris, they destroyed most of the checkpoints. She picked up her gun and went to the remaining checkpoints. Umaya was well trained in combat. She insisted on fighting with us. We were all hiding behind a wall as the fight became fiercer. I asked her to keep her head down, I could see Isis snipers deployed everywhere but she was busy shooting until she was hit in the chest. I put her in the car and rushed to the hospital. It was a single bullet in the chest. I tried to speak to her but she could not utter a word, she died within few minutes."