Commenting on an incident caused earlier in the day by the controversial Josko Joras, the ministry said that "the competent bodies of the Republic of Croatia acted in line with the law, and prevented an attempt to illegally cross the state border".
The ministry sent a protest note to the Slovene Embassy in Zagreb, emphasising that it was necessary to avoid similar cases in the future.
Joras, who has proclaimed himself a fighter for the southern border of Slovenia, caused two incidents at the Croatian-Slovene border at Plovanija on Wednesday morning.
Joras tried to illegally pass the border crossing but was prevented by the Croatian police.
After that, Joras, a member of the right-wing Slovene People's Party, was told to go to the Plovanija border police station but he resisted arrest which was why Croatian police officers had to bring him to the station.
"After an interview and the establishment of all facts, Josko Joras was released and charges will be pressed against him before a magistrate's court for his attempt to enter Croatia illegally," the spokesman for the Croatian Interior Ministry, Zlatko Mehun, told Hina on the phone on Wednesday.
The police also notified the Croatian Foreign Ministry and the State Border Commission of the incident at the borderline.
Before his attempt to illegally enter Croatia, Joras also called an expert from the District Court of the Slovene port of Koper, Dejan Zlajpah, to establish whether Joras's neighbour, Urban Cerar, had unlawfully built a parking lot in Mlini, Croatia, where the two have houses.
Joras accuses Cerar of trespassing his private property.
The Croatian police banned Zlajpah to inspect the situation on the ground given that he had no licence to perform a job on Croatian territory. After that the Slovene court expert peacefully left Croatia.
Mehun said that the Interior Ministry had sent requests to the geodetic survey departments of the two countries to establish who was competent to carry out this inspection, given that the ground plots which should be the subject matter of the survey of a court expert were entered into land books of the Croatian town of Buje.
The situation worsened when Joras's lawyer Daniel Starman labelled Croatian police officers as "occupiers".
Joras, who lives in Mlini, a village belonging to the town of Buje, came into the limelight a few years ago when he began causing incidents at the border from time to time. He does not want to recognise Croatia's jurisdiction over the territory where his house was built.
His party later in the day denounced the incident, expressing "outrage" at the conduct of the Croatian police describing it as "rude, unlawful and non-European".
The Slovene Foreign Ministry today handed over a protest note to the Croatian Embassy in Ljubljana over the incident involving Joras and the Croatian police.
"This move is yet another unilateral move by which Croatia is trying to prejudge a solution to the border issue," the Slovene note reads.