Gotovina was detained late on 7 December on Spain's Canary Islands. He was transferred to the Spanish capital Madrid on 8 December, where a Spanish tribunal ordered his immediate handover to the UN tribunal.
Reports quoting Spanish police sources said Gotovina is due to be transferred to The Hague aboard a Spanish military aircraft.
Croatian Prime Minister Ivo Sanader appealed for "calm and reason" after some 500 Gotovina supporters staged violent protests in Zagreb on 8 December.
Gotovina, 50, was indicted in 2001 on charges relating to the death of some 150 ethnic Serb civilians during a Croatian offensive in August 1995 in the self-declared Serbian republic of Krajina.
Many Croatian nationalists consider Gotovina a war hero.