The ministry said in a press release the operation was part of efforts to trace the runaway general. Two persons whose premises were searched are from the Zadar area and one is from Zagreb.
The ministry did not reveal their identity nor say who are the two on whose premises illegal arms were seized.
A source close to the police told Hina on Thursday that the houses of Zeljko Dilber in Zadar and Ante Maksan in Pakostane, in the wider Zadar area, were searched. The report was confirmed by eyewitnesses who said that 10 police cars arrived in front of Dilber's house about 0700 hours and that his mobile phone, computer and some other things were confiscated. Also in the morning, the police arrived at Maksan's house and took his computer, mobile phone and some planners.
These two comrades-in-arms and friends of Gotovina were allegedly interviewed by the police in Zadar, but the local police neither confirmed nor denied this.
The Interior Ministry only said that officers of the Zagreb and Zadar police departments were processing the three men on suspicion that they committed the criminal offence of assisting a perpetrator after he committed a crime.
At the end of its press release, the ministry said that after the police completed the investigation they would decide, together with state prosecutors, whether or not to press charges against some persons because of the criminal offences described above or some other crimes.
Zeljko Dilber and Ante Maksan are two of the five Croatian citizens who have been banned entry to the European Union on suspicion that they are assisting fugitive war crimes suspects. The other three men on this black list issued this June are Zeljko Bagic, Ljubo Cesic Rojs and Hrvoje Petrac.
Cesic Rojs told Hina the police had not visited him earlier today. Marijan Pedisic, a lawyer for businessman Hrvoje Petrac, who has been on the run since he was suspected of involvement in the abduction of General Vladimir Zagorec's son, also said that no search had been conducted on his client's premises today.
Nela Pedisic, a lawyer for Zeljko Bagic, said she had not yet contacted Bagic, and added that as far as she knew, no police arrived at his home.
Luka Misetic, a lawyer for Ante Gotovina, on Thursday afternoon voiced regret at the police searches of Gotovina's friends.
The police are not likely to trace General Gotovina after today's operations, the lawyer said in a press release, branding the police actions as an act of "intimidating and terrorising Gotovina's comrades-in-arms".
Gotovina has been beyond the reach of the Croatian judiciary and the Hague tribunal since July 2001, when the tribunal indicted him for war crimes against Serb civilians committed during Operation Storm in the summer of 1995.