An American F-16 fighter went down over western Serbia early on Sunday.
The Yugoslav media says it was shot down; Nato officials say an investigation into the crash is being carried out.
A second plane has also crashed in the Adriatic, while attempting to land on an aircraft.
Nato says the American AV8B Harrier crashed while on a training mission and that the pilot was rescued.
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Diplomatic Correspondent Humphrey Hawksley: "The F-16 is Nato's workhorse"[/font]The F-16 pilot was rescued by allied forces after he ejected from the plane over Serbia.
Lieutenant Colonel Michael Kaemnerer, at Nato military headquarters in Brussels, said the pilot was back at an allied base undergoing medical examination.
Belgrade city radio Studio B said that a Nato plane had been downed near Sabac, a town 80km (50 miles) west of Belgrade.
The radio station quoted unofficial sources as saying that the aircraft had been shot down at around 0300 local time (0100 GMT) on Sunday.
Aircraft losses disputed
The warplane was the second Nato has acknowledged lost in action over Yugoslavia since the air campaign started.
An American F-117 Stealth fighter crashed over Yugoslavia on 27 March, three days into the campaign. The pilot of that plane was also rescued.
A handful of unmanned drones have also gone down.
The Serb media regularly reports the shooting down of Nato aircraft, but these claims have been denied by the alliance. Many of the F-16s flown by the alliance have been based at Aviano in Italy.
source:BBC news