The two states have been embroiled in on-going tensions since Kosovo declared independence from Serbia in 2008 after a violent struggle.
A former Serbian province, Kosovo unilaterally declared independence in 2008 which came after the break-up of the former Yugoslavia and conflict in 1998-1999 in which North Atlantic Treaty Organisation attacked Serbia, killing many civilians.
Belgrade played down any controversy saying, "In a political sense, this train is no novelty, because it is only an extension of a railway line which has been functioning for 10 years now", said Marko Djuric, Serbian Government Office for Kosovo and Metohija. The train, which had been painted with Serbian national colors and the phrase "Kosovo is Serbian", cut short its journey amid fears it was under threat of violence.
Serbian prime minister Aleksandar Vucic said he ordered the train to stop before reaching Kosovo's border.
"This was an ambition to provoke a conflict, to start a wider conflict in this territory that we consider as ours", Vučić told reporters in Belgrade according to the New York Times.
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NATO-led troops are controlling Kosovo's borders following an intervention in 1999 to stop a bloody Serbian crackdown against ethnic Albanian separatists.
"We sent a train, not a tank", Vucic said, adding that he has informed the European Union and will speak to Russian Federation and the USA about the incident. The train was returned to Belgrade in order not to put the passengers at risk.
Kosovo President Hashim Thaci said Saturday on his Facebook page that Kosovo respects the freedom of movement of people and goods but a train covered in nationalist banners that violate Kosovo's constitution and laws "is completely unacceptable". Kosovo is recognized by over 100 United Nations member states. "This is a provocation towards Kosovo, which shows that Serbia has openly shown its aggressive policy, which endangers the sovereignty and territorial integrity and national security" of Kosovo. Northern Kosovo, where Mitrovica is situated, is home to a Serb minority of around 40,000 to 50,000 people who do not see Pristina as their capital.
Serbia said it was merely "a mobile exhibition presenting our cultural heritage". Last week, French authorities arrested former Kosovo Prime Minister Ramush Haradinaj on a Belgrade arrest warrant accusing him of war crimes.
Kosovo has called the warrant not legitimate and urged France to ignore it.