Isis rebels have been methodically hunting down non-Sunnis and those opposed to the militants, refugees from the rebel-held towns have told the BBC.
Isis demanded officials and soldiers pledge allegiance to the caliphate they recently declared or face execution.
More than one million Iraqis have fled their homes over the month as Isis seized Mosul, Tikrit and other cities in the north-west.
At least 2,461 people were killed in June, the UN and Iraqi officials say.
In other developments on Thursday:
Iraqi military officials denied that troops had abandoned positions along the border with Saudi Arabia, who had reportedly deployed 30,000 soldiers along the frontier.
Turkey announced that a group of 32 Turkish lorry drivers seized last month in northern Iraq by Isis had been handed over to Turkish diplomats. A group of 49 other Turkish citizens are still being held by the rebels.
India said 46 Indian nurses being held by militants in Tikrit were safe, but were being forced to move to a new area. It added that 40 Indian construction workers seized near Mosul were still being held, but were also unharmed.
The refugees in the Kurdish-controlled town of Sinjar, near Tal Afar, told the BBC's Quentin Sommerville that towns and villages they had fled were now being systematically cleared by Isis (the Islamic State in Iraq and the Levant).
|Iraqi children who fled fighting near Mosul prepare to sleep on the ground|
with their family in Khazair, Iraq. Photo: 3 July 2014
More than one million Iraqis have been displaced by the fighting over the past month
|Iraqi soldiers at Arar, near the Iraqi border with Saudi Arabia (28 June 2014)|
"For Shias, if they cannot be exchanged for prisoners, [the Isis rebels] would simply cut off their heads," said Hassan, a Kurd who had spent 16 days in captivity until his family paid £30,000 ($51,500) for his release.
Bashar al-Khiki, provincial leader who fled Mosul, said that the jihadists were "collecting information about people and compiling a database in order to identify those who work for the government or security forces".
"If they don't repent and pledge their allegiance to the caliphate, they will be killed. A lot of these people have disappeared in Mosul," he added.
Human rights groups have reported that Isis militants have been going neighbourhood to neighbourhood in Mosul, deliberately targeting non-Sunnis and those opposed to them.
Isis last week declared it was establishing a caliphate on the territories under its control in Syria and Iraq.