A spokesman for the EU's rule of law mission Eulex said two of the men were current members of the Nato-trained Kosovo Security Force (KSF).
No details were given of the charges against the three suspects.
But reports suggest the case relates to the murder of two supporters of moderate politician Ibrahim Rugova.
Rugova, who died of lung cancer in 2006, served as Kosovo's first president after its ethnic Albanian majority broke away from Serbia in 1999.
"The suspects are charged with war crimes against the civilian population," said Eulex spokesman Blerim Krasniqi, quoted by Reuters news agency.
The three, he added, were former members of the Kosovo Liberation Army (KLA), the ethnic Albanian rebels who fought the Serbian authorities during the war, which ended when Nato intervened