Earlier, a few dozen Serb railroad workers blocked passage of a freight train on the line, saying they would not work for Kosovo's railway company and demanding to be transferred to Serbia's state-owned railroad.
The railroad's surprise move is likely to increase tensions between the Serbs and Kosovo's authorities and NATO peacekeepers. It is in line with the Belgrade government's instructions to Kosovo's Serb minority to shun any contact with the Pristina government and to work directly with Serbia instead, after Kosovo declared independence two weeks ago.
Kosovo officials dismissed Serbia's move.
"We are promising that in any case ... we will control the whole of Kosovo's territory," Deputy Prime Minister Hajredin Kuqi told The Associated Press.
Hundreds of Serb policemen have handed over their badges and weapons rather than submit to Kosovar authorities. Serb protesters have torched border crossing points with Serbia and have blocked ethnic Albanians from working in courts in the northern area.
It was not clear how the takeover of the rail line by Serbia's railroads would be carried out. Serbia, which rejects Kosovo's independence declaration, has long claimed ownership of much of Kosovo's infrastructure, including power plants and railways.
Belgrade has ruled out military action to reclaim Kosovo, but has said it has a secret "action plan" to deal with the breakaway province. Officials have said Serbia would seek to retain control of Serb-dominated areas in northern Kosovo.
Belgrade and its ally Russia maintain that the U.N. Security Council has not authorized a European Union mission that is meant to replace the current U.N. administration.
Russia's Foreign Ministry on Monday also protested the creation last week of the 15-nation International Steering Group for Kosovo, whose mission is to help guide Kosovo's democratic development. Moscow said it violates U.N. decisions and could lead to "unpredictable consequences."
"We think the creation of the group goes against U.N. Security Council resolution 1244 and internationally agreed principles" for handling Kosovo's future, ministry spokesman Mikhail Kamynin said in a statement.
Serbia lodged a complaint about the steering group with the United Nations.
The group includes the United States, Turkey and 13 other European countries - all of which have recognized Kosovo's Feb. 17 declaration of independence from Serbia.
The group appointed Pieter Feith to be the International Civilian Representative for Kosovo. He is also the European Union's representative in Kosovo, and heads the 1,800-strong EU mission for Kosovo. Serbian officials have refused to deal with him.
Archbishop Artemije, who heads Serbia's Orthodox Church in Kosovo, ordered his clergy on Monday to cease all contacts with Kosovo's authorities and with the coming EU mission.
Serbia lost control of Kosovo after a brief air war in 1999, when NATO stopped the forces of Serbia's former strongman Slobodan Milosevic from cracking down on ethnic Albanian separatists.