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With Serbian forces set to leave by midnight on Tuesday, civilians fear reprisals from the Kosovo Liberation Army (KLA) and returning Kosovo Albanians.
A large convoy reportedly left Pristina overnight, despite Nato assurances that Serbs would be protected.
The exodus began as tension grew between retreating Serbian forces and KLA guerrillas, in areas under the control of the K-For peacekeeping force.
A number of incidents were reported in the city in a second night of violence between the two groups.
British military sources said KLA members apparently took a Serb hostage and shot and killed him. K-For paratroops later arrested five KLA members.
And a Nato spokesman said that a rocket propelled grenade was fired on Tuesday near Pristina airport, which Russian troops unexpectedly took control of last Saturday.
It caused no damage or injuries. The spokesman did not say who fired the grenade.
KLA welcomed back
Kosovo Albanians have been welcoming the return of armed KLA soldiers to Kosovo's second largest city, Prizren, and treating them as heroes.
But some of Prizren's Kosovo Albanians jeered, spat and threw stones at the retreating Serbs, most of whom were heading north into Serbia.
German K-For troops, who arrived at the weekend, stood guard outside a church for most of the night, where Serbs too frightened to leave took refuge.
(Click here to see a map showing timetable of Serb withdrawal and Nato's planned movements)
Nato says some 14,300 K-For troops have now entered Kosovo - and will guarantee Serb safety.
Italian troops have entered the city of Pec, the seat of the Serbian Orthodox Church in Kosovo, and scene of some of the grimmest accounts of slaughter in recent months.
Yugoslav troops withdrew from the city on Monday after a spree
of house torchings and alleged rapes.
Refugees warned to wait
Many Kosovo Albanian refugees are returning to the province, despite warnings from the United Nations that their safety cannot be guaranteed.
Officials from the UN refugee organisation, the UNHCR, say it could be several weeks before Nato troops have had a chance to clear the region of mines and booby traps.
But several hundred refugees have already crossed the border from neighbouring Macedonia, and their number is expected to grow.
Aid workers say they looked on helplessly as hundreds of refugees queued at checkpoints in the scorching sun to go home.
Some 20,000 displaced Kosovo Albanians have been found inside Kosovo, hiding in the mountainous area west of Pristina.
One official said there could be up to 500,000 people "living hand to mouth" in desperate need of help.
The refugees have been fleeing their homes over the last three months, following systematic attacks by Serb forces.
Evidence of massacre
Nato troops have sealed off a cemetery in southern Kosovo where they suspect the bodies of Kosovo Albanians massacred by Serbs may be buried.
The cemetery, at the village of Kacanik, contains about 35 fresh graves.
People in the area are alleging that Serb paramilitaries carried out an ethnic cleansing operation in a nearby village just over two months ago.
They said the young and fit managed to escape into the hills, but the elderly and infirm were shot dead.
Pressure mounts on Russia
As Russian troops continued to occupy Pristina airport in defiance of Nato plans, US Secretary of State Madeleine Albright added her voice to European calls for Kosovo to come under the sole command of the Nato-led peacekeeping force.
Mrs Albright said the Russians would not be given control of their own sector in Kosovo, and must accept the Nato command structure.
President Clinton and President Yeltsin have discussed the issue twice on the telephone, and their defence ministers will try to clarify Russia's role at a meeting in Finland later this week.
To add to the pressure on Russia, Bulgaria has said it will only consider a request for Russian troops to cross Bulgarian air space once the current stand-off with Nato is settled.
A similar Russian request to Hungary has been made subject to parliamentary approval - the vote is expected later this week.
More Russian peacekeepers left Bosnia on Tuesday and were heading toward Pristina airport, according to the Moscow news agency, Tass.
(click here to return)
Picture gallery: Changing face of Kosovo
(14 Jun 99 | Europe)
Kosovo Crisis Centre
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