County Prosecutor Bozidar Piljic confirmed on Friday that the probe was launched to establish if the media reports were credible.
According to Piljic, the Office of the Prosecutor initiated pre-investigative proceedings as soon as Croatian media carried reports on Stojanovski's involvement in the 1991 attacks on Vukovar.
The reports on Stojanovski's service with the JNA appeared after he officially visited Croatia on 18 November, when Croatia commemorates the fall of Vukovar.
"After the Office of the Chief State Prosecutor yesterday sent us a request for launching an investigation into the Stojanovski case, I immediately ordered the police to investigate the media reports and gather information from persons who have information on Stojanovski's role in the aggression against Vukovar," Piljic said.
The police have a 30-day deadline to finish the job and inform prosecutors of their findings. The prosecutors will then decide whether there are grounds for issuing an indictment against Stojanovski.
The association of former Croatian prisoners of Serb-run concentration camps on Wednesday presented Croatian President Stjepan Mesic and Prime Minister Ivo Sanader with a request for issuing an indictment against Stojanovski.
The former prisoners claim that during the siege of Vukovar Stojanovski was the commander of the JNA military police who on 18 November 1991 arrested several Croatian soldiers and took them to Vucedol outside the town. The fate of those soldiers has been unknown since then.
The former prisoners accuse Stojanovski of verbally abusing captured Croatian soldiers as they were transported to the prison in Sremska Mitrovica, Serbia.