Human rights organisations have long pressed the Croatian government to find the perpetrators behind the killings of ethnic Serbs in the eastern Croatian city of Osijek in late 1991 and early 1992.
"After 15 years we have gathered information about the killings of civilians in Osijek and the perpetrators who tied the victims' hands, put sellotape on their mouths and threw them into the Drava river," the state news agency quoted Vladimir Faber, the eastern Osjecko-Baranjska county police chief, as saying.
A police spokeswoman said that the former soldiers were arrested on suspicion of torturing and killing a number of civilians, mostly Serbs.
Osijek, which has a population of around 100,000 people, was a target of heavy shelling by rebel Serbs and the Yugoslav army at the beginning of the war.
Croatia has made efforts to come to terms with war crimes committed by its own troops in recent years as it advances towards membership of the European Union.