The UNHCR says they were from Hawiga District and 12 were killed by the jihadist group.
It followed a statement on Thursday from the Iraqi Observatory for Human rights, which claimed 1,900 civilians had been captured by more than 100 IS fighters.
They were using the people as human shields against attacks by Iraqi Security Forces, the statement said, adding tens of civilians had been executed, and six burnt.
The UNHCR said it had "received reports that ISIL captured on 4 August up to 3,000 IDPs (internally displaced people) from villages in Hawiga District in Kirkuk Governorate, trying to flee to Kirkuk city.
"Reportedly, 12 of the IDPs have been killed in captivity."
Millions of people have been displaced since IS took control of large areas of Iraq and neighbouring Syria in 2014.
The United States has been leading a military coalition carrying out airstrikes against IS, and the group's grip on some towns has been broken.
But it still controls Mosul in Iraq and Raqqa in Syria.
The UN has appealed for more than £200m to prepare aid in the event of an assault on Mosul, as well as up to £1.5bn to deal with the aftermath.
So far it has received nothing, according to the UN Financial Tracking Service.