It comes after massive bombing of rebel-held eastern sections of the city and a regime advance forced thousands of civilians to take emergency routes out of the area.
UN spokesperson Rupert Colville said that family members have reported losing contact with the men - who the UN says are between the ages of 30 and 50 - after they fled bombing and regime advances of opposition-held areas around a week ago.
"While it's very difficult to establish the facts in such a fluid and dangerous situation, we have received very worrying allegations that hundreds of men have gone missing after crossing into government-controlled areas," Colville said.
He added that the UN High Commissioner for Human Rights is also concerned by claims that some civilians trying to flee are being blocked by rebels, and in some cases being fired upon.
Opposition activists mostly deny these allegations, saying that regime forces have fired on civilians entering "evacuation corridors".
Colville echoed Russian and regime claims that "civilians are being used as pawns and prevented from leaving".
The Aleppo council governing opposition areas has proposed a five days ceasefire to allow any civilians wishing to to leave East Aleppo under safer conditions.
They also called for the safety of the evacuees and that assurances they wouldn't be arrested of disappeared by regime forces - something which is said to be preventing more civilians from leaving the war zone.
There are around 100,000 civilians trapped or taking refuge in shrinking areas of rebel-held East Aleppo, where Russian and regime artillery barrages and constant bombing have killed 800 people in less than a month.
Despite a ceasefire announced by Russia, regime shelling has continued.
Agencies contibuted to this story.