The anti-Serb chants were heard during Kosovo's first competitive "home" international since being admitted to FIFA in May, although the game -- which Croatia won 6-0 -- was played at Shkoder, in neighbouring Albania, because of a lack of facilities in Kosovo itself.
Kosovo's campaign to join FIFA faced fierce opposition from Serbia, from which it declared independence in 2008.
Croatia had already been ordered to play their first two home matches in the World Cup qualifiers behind closed doors because of trouble at previous games, including racist chanting.
They played Turkey in an empty stadium in September and spectators will also be barred when they host Iceland in November.
FIFA did not say when the hearing would take place.
(Writing by Brian Homewood; additional reporting by Zoran Milosavljevic in Belgrade; Editing by Neville Dalton)
