The returnees, who fled violence during and after the Islamic State group's 2014 seizure of swathes of Iraq, had sought refuge at displacement camps in the northern province of Nineweh.
Since August 23, Iraqi authorities have bussed about 300 families, an estimated 1,600 people, from the three camps to their provinces of origin.
The transfers took place despite humanitarian groups' concerns that the families had no homes or access to services and may be targeted by their home communities for perceived links to IS.
The UN said Monday returnees had "expressed fears that they would be threatened upon their return, and had reportedly received threatening phone calls from community members in their areas of origin warning against return."
"Despite such concerns, security actors confiscated the (displaced people's) civil identification, informing the families that their documents would only be returned once they boarded the convoy," it said in a statement.
More than 1.6 million people remain displaced in camps, unfinished structures or rented apartments across Iraq, nearly two years after the country declared victory over IS.
The government has stressed its policy is for all those displaced to return home and for camps to be shut.
Last week, AFP journalists witnessed transfers from the Hammam al-Alil camp in Nineweh province of hundreds of Iraqis originally from Kirkuk, further south.
Women and children, some of them crying, were loaded onto buses by security forces. Some said they did not know where they were being taken.
The transfers often happened "with little notice or apparent planning," the UN's Iraq humanitarian coordinator, Marta Ruedas, said on Monday.
"I am concerned about the lack of organisation and advanced communication with affected communities and humanitarian partners," she said.
In some cases, the UN said, security forces denied families entry to camps in their home provinces, displacing them a second time.
In the worst case of violence against returnees so far, three hand grenades were thrown into the Basateen camp in Iraq's Salahaddin governorate on Sunday, a day after the arrival of 150 displaced families from Nineweh.
"The grenades caused no damage, injuries or casualties (but) are a cause of great concern for the safety of the camp residents," the UN said.
Other rights groups have already sounded the alarm, including Amnesty International, which has called the returns "premature" and urged Iraqi authorities to halt them immediately.
The Norwegian Refugee Council (NRC) called on the government to double down on reconciliation efforts to heal lingering resentment from the fight against IS.