The chanting can be clearly heard on video reports. Visiting Croatia supporters shouted "ubij" (kill) and Kosovo Albanian fans shouted "Srbina" (the Serb) in response.
Fans of both teams also allegedly shouted "hang the Serbs," and Croatian fans reportedly shouted fascist slogans.
BREAKING: During match between Kosovo and Croatia, played in Albania, both sides shout "Kill The Serbians, Kill the Serbians" pic.twitter.com/us8sB32gl0— Vincent Triest (@VincentTriest) 6 октября 2016 г.
The game with Croatia is Kosovo's first qualification match for a major competition since it was recognized by the Union of European Football Associations (UEFA) in May. The controversial decision was opposed by 24 UEFA members, 28 were in favor and two abstained.
The Albanian-dominated government of Kosovo unilaterally declared independence from Serbia in 2008, and the territory has been allowed by FIFA to take part in friendly football matches since 2014.
Croatia and Kosovo fans also shouted anti-Serb hate speech in the streets of Skadar before the game.
Thursday's match was a Kosovo home tie which took place in the Albanian town of Skadar because the Kosovo FA is redeveloping its stadium in the Kosovo capital Pristina, which doesn't currently meet the requirements for competitive international games.
Croatia won the game 6-0, in part thanks to a first-half hat-trick from Juventus striker Mario Mandzukic. The result leaves them with four points in joint first place with Iceland in Group I, from which one or two teams will progress to the 2018 World Cup Finals in Russia.
While Kosovo is a newcomer to international competitive football, the Croatian FA has been sanctioned several times because of the behavior of its fans, and has been forced to pay around 750,000 euros ($839,000) in fines to UEFA and FIFA over the past five years.
This year the Croatian FA has also been fined 135,000 euros and forced to play two matches behind closed doors as punishment for the racist and violent behavior of fans during friendly games against Hungary and Israel in March.