Some 30 NATO peacekeeping soldiers were injured on Monday in clashes with Serb protesters in the northern Kosovo town of Zvecan, where Djokovic's father grew up.
Serbs, who comprise a majority in Kosovo's north, have never accepted the country's 2008 declaration of independence from Serbia.Â
They still see Belgrade as their capital more than two decades after a Kosovo Albanian uprising against repressive Serbian rule. Ethnic Albanians make up more than 90 per cent of the population of Kosovo as a whole.
Monday's clashes came as ethnic Albanian mayors took office in Serb-majority areas following elections that the Serbs had boycotted.
"Kosovo is the heart of Serbia. Stop the violence," 22-time grand slam champion Djokovic wrote in Serbian on a TV camera at the French Open in Paris.
He later explained that he was against war but defended his statement and described Kosovo's situation as a "precedent".
"As a son of a man born in Kosovo, I feel the need to give my support to our people and to entire Serbia," he told reporters.
"My stance is clear: I am against wars, violence and any kind of conflict, as I've always stated publicly. I empathise with all people, but the situation with Kosovo is a precedent in international law," he said.
Kosovo tennis federation president Jeton Hadergjonaj said in a statement: "The comments made by Novak Djokovic at the end of his Roland Garros match against Aleksandar Kovacevic, his statements at the post-match press conference and his Instagram post are regrettable."
Hadergjonaj accused Djokovic of using his status as a well-known personality to stir tensions.
"Novak Djokovic was already the author of similar actions in the past," the statement added.
"Despite a general message against violence, the statement 'Kosovo is the heart of Serbia' and further statements after the match, made by such a public figure, on the occasion of a worldwide event like the French Open, directly result in raising the level of tension between the two states, Serbia and Kosovo."
A source told Reuters the French Tennis Federation did not see Djokovic's action as "detrimental to the best interests of the tournament", as per the Grand Slam rulebook.
