Ljubisa Beara, who was a colonel and the chief of security for the Bosnian Serb army main staff during Bosnia's Srebrenica massacre, was extradited late on Saturday to the UN war crimes tribunal in The Hague, a government statement said.
Beara was indicted for allegedly killing Muslim prisoners and forcing the transfer of tens of thousands of women and children from the enclave.
He took part in the decapitation of 80 to 100 Muslims in the town of Potocari on 12 July 1995, the indictment alleges.
Beara is accused of being part of a "joint criminal enterprise" headed by General Ratko Mladic, then commander of the Bosnian Serb army, who is now one of the tribunal's two most-wanted men.
Beara surrendered "to protect the interests of the state and those of his family," the statement said.
Serbia-Montenegro, the successor state to Yugoslavia, has been under mounting international pressure to arrest and extradite Mladic and 15 other war crimes suspects to the UN tribunal.
The US and the European Union have made future financial and political support conditional on the extradition of Mladic and the others.
The government said Beara insisted he should "go to The Hague immediately".
He was accompanied on his flight by Serbian justice minister Zoran Stojkovic, government spokesman Srdjan Djuric said.
Slobodan Milosevic is on trial
for the Srebrenica massacre
Among others indicted for the Srebrenica killings is Slobodan Milosevic, who was president of Serbia and later president of the Yugoslav federation and is now standing trial for alleged crimes in Croatia, Bosnia and Kosovo during the turbulent 1990s.
Another Srebrenica suspect is wartime Bosnian Serb leader Radovan Karadzic who, along with Mladic, tops the most-wanted list.
The Srebrenica killings occurred in July 1995, just a few months before the end of Bosnia's war, when Serb soldiers overran the eastern Bosnian enclave under the protection of an ill-equipped and understaffed battalion of Dutch army soldiers.
It was the worst civilian massacre in Europe since the second world war.
So far, the remains of more than 5000 Srebrenica victims have been exhumed from various mass graves across eastern Bosnia.