"This move is yet another unilateral move by which Croatia is trying to prejudge a solution to the border issue," the note reads.
The Slovene ministry also believes the treatment of Joras by the police was contrary to a joint statement which the two countries' government had made on avoiding incidents.
The ministry described it as territorial claim to Slovene territory.
Describing the backdrop of the incident the Slovene ministry asserted that Joras and his attorney Danijel Starman had been all the time on "Slovene territory".
The controversial Josko Joras, who has proclaimed himself to be a fighter for the southern border of Slovenia, caused two incidents at the Croatian-Slovene border at Plovanija on Wednesday morning, the Croatian authorities reported.
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.
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, 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 would be 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 was worsened when Joras's lawyer Daniel Starman labelled Croatian police officers as "occupiers".