"Forty-four people died, this is certain, and one survived," Hungarian police spokesman Laszlo Garamvolgyi told a news conference on Friday.
The crash occured 250km from the Hungarian capital Budapest and just 20km from the Slovak base in Kosice to which the troops were being flown to. The AN-24 aircraft took off from Kosovo's capital, Pristina.
In Kosovo, a Nato officer, who was not authorised to speak on the record, said the plane carried Slovak soldiers serving in the Nato-led peacekeeping force there. They were returning to Slovakia after six months' duty in the province.
About 100 Slovak troops serve in a battalion that patrols the boundary between Kosovo and Serbia.