The statement on January 12 by the EU office in Kosovo comes after a similar message from the United States last month.
The warnings come amid uncertainty whether Kosovo's parliament will put a vote on the court back on its agenda next week after shelving it on December 22 under U.S. and EU pressure.
The court -- the Specialist Chambers and Specialist Prosecutor's Office -- was established in 2015 to try ex-Kosovo Liberation Army (KLA) fighters alleged to have committed atrocities in the 1998-1999 war that led to independence from Serbia.
It has yet to hear any cases.
Kosovo media have said the court, based abroad in The Hague, could indict or call as witnesses some current government officials.
It was set up in the Netherlands to minimize the risk of witness intimidation and judicial corruption.
Prime Minister Ramush Haradinaj, President Hashim Thaci, and parliamentary speaker Kadri Veseli are former KLA commanders.
Based on reporting by AP and Reuters