Nikolic raised the warning after Kosovan officials prevented the Serbian train, which contained signs saying "Kosovo in Serbian," from entering Kosovo over the weekend.
"Yesterday, we were on the verge of clashes," he said after meeting with Serbia's top security body.
Nikolic accused Kosovo Albanians of "wanting war," adding:
"We are a country which has to protect its people and its territory."
Kosovo, which has a majority population of ethnic Albanians, declared independence from Serbia in 2008 after a bloody war and NATO intervention, however Serbia has never recognized Kosovo's independence, considering the former province to still be a part of its territory, while Belgrade also supports the Serb minority living in Kosovo.
Kosovo: Train a 'Message of Occupation'
The latest spat occurred after the Serbian train left Belgrade for Kosovo's northern town of Mitrovica on Saturday, January 14.
However the train was stopped while still in Serbia after Pristina said it had deployed special forces to prevent the train from crossing the border.
#Kosovo gov stopped illegal train to enter our territory. Serbia is a source of conflict, endangering peace & stability!— Enver Hoxhaj (@Enver_Hoxhaj) January 14, 2017
Leaders in Kosovo viewed the train as a provocation, saying it sent "a message of occupation."
"The institutions of the Republic of Kosovo will always undertake such actions to protect the country's sovereignty and not allow machines that will provoke with a message of occupation," Kosovo Prime Minister Isa Mustafa said.
Republic of Kosovo fully committed to freedom of movement but will not allow provocation. (Full Press Statement: https://t.co/sdJmMnSdQ2)— Isa Mustafa (@IsaMustafaKS) January 14, 2017
Concerns Over Ethnic Tension
While always tense, relations between Serbia and Kosovo worsened earlier this month when former Kosovo Prime Minister Ramush Haradinaj was arrested in France after Serbia had issued an arrest warrant, accusing him of committing war crimes.
Ethnic Albanians make up 90 percent of Kosovo's 1.8 million population, while it's also home to around 50,000 Serbs.
The development also comes amid ethnic tension in Bosnia, with officials from the Serb-dominated Republika Srpska (RS) defying EU, US and Bosnian warnings not to celebrate the region's self-proclaimed independence day on January 9.
Despite the holiday being declared unconstitutional by the Bosnian High Court, RS officials took to the streets to demand more autonomy.