The British Puma helicopter came down in the mountains at Kranacia, south-west of Pristina, at 1345GMT on Monday.
Seven people were on board - three crew and four passengers - and the five survivors were injured in the crash.
The dead men were named by the MoD as the helicopter's two pilots, 28-year-old Captain Andrew Crous of the Army Air Corps and RAF Fl Lt James Maguire, 31, both based at RAF Benson.
"It appears that the aircraft had to execute an emergency landing in heavy rain, low cloud and mountainous terrain," said an MoD spokesman.
"There is absolutely no evidence of any hostile action."
Poor visibility
The five injured - four soldiers from the 2nd Royal Tank Regiment and an RAF loadmaster - are being treated at a US field hospital at Camp Bondsteel. There injuries were said not to be life threatening.
All the personnel involved were part of Task Force Cambrai which is involved in interdiction operations on the Kosovo-Macedonian border against ethnic Albanian insurgents.
Major Fergus Smith, a spokesman for British peacekeeping forces in Kosovo, said an inquiry was being launched into the accident.
K-For Lieutenant Colonel Nick Brehaut said a British inquiry team was being sent out to investigate the circumstances of the crash.
The aircraft crashed in an area where there has been an upsurge in guerrilla activity connected with the emerging insurgency in neighbouring Macedonia.
Nato officials said the helicopter went down while flying above mountainous terrain. They said visibility was poor, with heavy rain and low cloud.