Serbia had styled the train as a bid to revive the first rail service from the Serbian capital to the mostly ethnic Serbian north of Kosovo since a bloody war 18 years ago that propelled Kosovo towards independence.
But Kosovo denounced the scheme as a provocation and an attempt to damage its territorial integrity. Its president, Hashim Thaci, called on "leading officials to take the necessary measures to stop this train, which threatens Kosovo's sovereignty".
"I decided to stop the train at Raska to avoid a conflict and save lives," Vucic told a press conference in Belgrade.
He accused the Kosovo government of sending police units to the north of the territory to "provoke a wide-ranging conflict".
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"Serbia wants peace... But I ask the Albanians of Kosovo not to try attacking Serbs in Kosovo because Serbia will not allow it," Vucic warned.
Some 13,000 people were killed in the 1998-1999 war, sparked by clashes between the forces of the rump Yugoslav state -- Serbia and Montenegro -- and Kosovo separatists. The conflict ended when NATO carried out an air campaign against Serbia.
Kosovo unilaterally declared independence in 2008, but Serbia and its ally Russia have yet to recognise its sovereignty.
The train, painted in the red, blue and white of the Serbian flag, was decorated inside with replicas of religious icons from Serbian Orthodox monasteries located in Kosovo. It also bore the inscription: "Kosovo is Serbia".
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