Tom Collins, a spokesman for the International Security Assistance Force, said: "It was not enemy fire related. The pilot was able to radio in that he was having engine problems. We're confident it was not due to enemy action."
There were reports that the helicopter was a Chinook, which would have the capacity to carry around 30 people, but the multinational force would not say how many people were on board.
The helicopter went down near a road in the Shahjoi district of the province of Zabul, according to residents there.
Dilber Jan Arman, Zabul's provincial governor, said the helicopter fell in the Hassan Kariez area of Shahjoi.
The governor said it was possible that the "helicopter crash was due to bad weather. Locals said the road was sealed for about an hour and a half as foreign soldiers moved into the area.
James Bays, Al Jazeera's correspondent in Afghanistan, said: "The Chinook is very much the workhorse of the American military and also of Nato operating in Afghanistan."
Besides ferrying people from one place to another, he said, the Chinook is "also used to carry vital supplies and equipment - these are transported to forward areas by air rather than by road because the situation on the ground isn't safe and the are worried about ambushes, roadside attacks and suicide bombs".
Also on Sunday, the Nato-led force said British forces attacked and cleared a "major Taliban extremist headquarters" in the southern province of Helmand in an overnight operation.
It did not say how many fighters were killed.
The British-led operation in Helmand overnight destroyed three major compounds and a tunnel complex that linked them, an ISAF statement said without estimating Taliban casualties.
Separately, Afghan authorities reported the killing of seven Afghans in new unrest.
On the other hand, Al Jazeera's correspondent in Afghanistan quoted a Taliban spokesman as claiming the killing of six multinational-force soldiers in Kunar province in east Afghanistan.
The attack targeted a military base, the spokesman said.
In the eastern province of Paktia, Abdul Rahman Sarjang, the police chief, said that about 25 armed men who had taken refuge in a village late on Saturday dragged five worshippers from a mosque and shot them, killing two.
The mob moved on to another police post, attacking and wounding a policeman who later died, he told AFP, labelling the fighters "opponents of the government", which Afghan officials use to mean Taliban fighters.
In the western province of Farah, a remotely detonated bomb struck a police vehicle returning from an operation to eradicate illegal opium crops.
Two policemen were killed and three wounded, Mohaidin Khan, the provincial governor, said, blaming the Taliban.