Croatian state television said Perkovic had been handed over to German authorities at Zagreb airport on Friday (24.01.2014).
The 68-year-old was taken directly from his home in the morning and flown to Munich aboard a commercial flight.
Germany placed Perkovic on its wanted list in 2005, accusing him of involvement in the 1983 murder of Yugoslav defector Stjepan Djurekovic. The Yugoslav secret service, of which Perkovic was a member at the time, is alleged to have been behind the killing in the Bavarian town of Wolfratshausen.
Perkovic, whose defense counsel has lodged a series of appeals against the extradition, has denied any part in the murder and has said that he has no chance of a fair trial in Germany.
'Classic intelligence work'
Croatia's Supreme Court on Tuesday gave the go-ahead for Perkovic to be handed over, ruling that his complaint was unfounded. The extradition was initially approved on January 8, after a European Arrest Warrant was issued.
Speaking to DW ahead of his extradition, Perkovic asserted his innocence. "I am not connected with any murders," he told DW. "I said long ago that I had nothing to do with the murder of Djurekovic or anyone else. I did classic intelligence work. I focused on protecting Croatian territory and Croatian citizens."
Shortly before Croatia's accession to the EU on July 1 last year, Zagreb had changed the law to limit the extraditions only to crimes allegedly committed after August 2002. After the threat of sanctions from Brussels, Croatia said in October it would withdraw the stipulation and Perkovic was arrested on New Year's Day. Germany is also seeking the extradition of Perkovic's predecessor, Zdravko Mustac.
Croatia was a high-ranking official in communist Yugoslavia's secret service in the 1980s and helped set up Croatia's own intelligence agency when the country became independent in the 1990s.
rc/bk (AP, Reuters, dpa)