Croatian ex-general Ante Gotovina, arrested at a luxury hotel on the Canary island of Tenerife on Wednesday night, left a military base near Madrid on Saturday morning aboard a Spanish military plane headed for Rotterdam.
The source at the military base at Getafe outside Madrid said the plane had taken off.
Gotovina was taken to the base under police escort from Madrid's Soto del Real prison earlier on Saturday.
One of three top fugitive suspects from the 1990s Balkan wars, Gotovina, 50, faces charges at the UN tribunal relating to the death of about 150 ethnic Serb civilians during a Croatian offensive in the Serb-held Krajina region in 1995. He was expected to plead not guilty.
He has been on the run since his indictment in 2001 by the International Criminal Tribunal for the former Yugoslavia (ICTY), based in The Hague.
Very mobile suspect
Spanish Interior Minister Jose Antonio Alonso said on Friday Gotovina had travelled through Asia, Latin America and Europe before Spanish police tracked him down in the Playa de las Americas resort in Tenerife.
He had 12,000 euros ($14,000) in cash and two false passports filled with visa stamps.
Gotovina supporters gathered in
Zagreb after his arrest in Spain
"(This) allows us to deduce that this person was very mobile, he had stamps from Tahiti, Argentina, China, Chile, Russia, Czech Republic and the last stamp is from the island of Mauritius," Alonso told a news conference.
Spanish police, after a tip-off from international police organisation, Interpol, detected Gotovina was in the Canary Islands in October, he said. They later tracked him down to a luxury hotel where nine police officers arrested him while having dinner with a friend.
Croatian newspaper Jutarnji List reported on Friday that Croatian counter-intelligence service POA had first located Gotovina, on the run since he was indicted in 2001, in the Canary Islands in spring last year.
It said Zagreb had managed to trace Gotovina's mobile phone calls to his wife, lawyer and a close friend. The net tightened after the arrest in Greece in August of a Croat businessman suspected of helping Gotovina financially, it said.
Croatia presented evidence of Gotovina's stay in Spain to chief UN war crimes prosecutor Carla del Ponte when she visited Zagreb in September, and told her that Zagreb was in touch with Spanish security services, the daily said.
Croatia's involvement was confirmed by del Ponte, who said on Thursday: "We worked together very closely not only with Croatia but with the authorities in Spain".
Gotovina spent the night in a Madrid jail after Spain's High Court ordered his transfer to the UN court, set up to try war crimes committed as Yugoslavia fell apart in the 1990s.
Calls for Serb cooperation
Gotovina is the last wanted war crimes suspect from Croatia, and his arrest will ease Zagreb's path to joining the European Union, which was long sceptical over how hard Zagreb was trying to hunt a man many Croats consider a national hero.
"Croatia said it would do it and has done it"
French Foreign Minister
The arrest brought renewed US and EU calls for the capture of Karadzic and Mladic.
French Foreign Minister Philippe Douste-Blazy said Serbia should follow Croatia's example of cooperation.
"Croatia said it would do it and has done it," he said in Belgrade where he was due to meet Serb leaders. "Asking for cooperation is one thing, getting it is another."
Germany's ambassador in Belgrade Andreas Zobel said the EU's patience with Serbia and its sister republic Montenegro, sometimes accused of harbouring Karadzic and Mladic or at least of reluctance to seize them, was "limited".
President Dragan Cavic of Bosnia's Serb Republic repeated a plea for the two to surrender to the Hague court.
"It needs to be understood that the institutions and the people of the Serb Republic have become hostages of this situation and it definitively has to end," Cavic told reporters.
Six Serbs or Bosnian Serbs are still on the run. Karadzic and Mladic face the gravest charges, of genocide for the Srebrenica massacre of 8000 Muslims and the siege of Sarajevo, which killed more than 10,000. They have eluded capture for a decade.
Until recently, Gotovina was so popular that posters of him, captioned "hero, not criminal", popped up all over Croatia.