Police also filed charges with the Split County Prosecutor's Office against Rajic for inciting Cesic to commit a criminal offence and for obtaining documents of false content under an assumed name.
The news was announced in a statement by the Ministry of the Interior, which did not reveal the names of the two men. Hina learned the names from a source close to the police who wished to remain anonymous.
The Split County Prosecutor's Office would not confirm or deny the news, saying that it could not reveal any details at the moment.
Cesic, who also held the post of assistant defence minister, is charged with abuse of office because he arranged for Rajic to be given fictitious employment in the Defence Ministry and free accommodation in a Defence Ministry building from June 30, 1994 to June 30, 1996, which cost the ministry 48,000 kuna (about 6,400 euros), the statement said.
Cesic held the rank of major general throughout that period.
The ministry said that a criminal investigation had been launched in cooperation with the Chief Public Prosecutor's Office after Rajic was arrested in Split in April 2003.
The purpose of the investigation was to determine the circumstances under which the suspect was hiding from the moment Croatia received the indictment from the UN war crimes tribunal in The Hague and the warrant for his arrest and to identify persons who had possibly assisted him in evading arrest and transfer to The Hague, according to the statement.
The investigation revealed that Rajic had obtained documents in the assumed name of Jakov Kovac in the central Bosnian town of Kiseljak in 1994 in order to conceal his identity. He used the documents to apply for and obtain Croatian citizenship. Rajic was issued a personal ID card in Omis, just southeast of Split, in 2003.
All information on how Rajic obtained false documents in the name of Jakov Kovac has been made available to Bosnian authorities, and the Croatian police are continuing the investigation in order to identify other possible helpers of Rajic.
The statement did not specify the Defence Ministry building in which Rajic had been hiding. Media have speculated that it was a military hotel in Split.
In October 1996, Globus weekly reported that Rajic was hiding in the "Zagreb" hotel in Split. The Defence Ministry filed a defamation suit against the weekly's former editor-in-chief Davor Butkovic and journalist Vlado Vurusic, after which the two were each given a year-long suspended prison sentence by the Zagreb Municipal Court in 1998.
Later on Thursday, Cesic dismissed the charges. "I did not find employment for Rajic. I was not in a position to do that, because I was in the field and not in the Defence Ministry at the time," he told Hina.
Cesic said that in 1994 he was in war zones in Croatia, and in 1996 he was with his 66th Regiment in Bosnia-Herzegovina where he was involved in construction projects. He added that he did not have the authority to give anyone employment at the time and that he was appointed assistant defence minister for economic affairs in 1998.
Cesic described the police charges as "a continuation of the political showdown" initiated by Prime Minister Ivo Sanader. He did not elaborate.
"Let them press charges. I will tell the truth in court and will say who gave Croatian diplomatic passports to persons indicted by the Hague tribunal," Cesic said.
Cesic said he had not been called for a police interview and that he did not know details of the charges against him.