Robert Pavlekovic, spokesman for the Istria Police Department, told Hina that the Austrian yacht had been checked at 1225 hours on Thursday in Croatian territorial waters, 0.7 nautical miles south of the border in the Bay of Savudrija, about 100 metres off the Kanegra campsite near Umag.
Pavlekovic said that it was not an incident but a regular check.
The Croatian Ministry of the Interior, however, said that Slovene police crossed the borderline in the Bay of Savudrija on Thursday.
"A Slovene police boat was noticed in Croatian territorial waters at about 1020 hours and after a warning it left our waters at about 1045 hours," Interior Ministry spokesman Zlatko Mehun said.
The Slovene People's Party (SLS), one of the four parties in the coalition government of Prime Minister Janez Jansa, said on Friday that "the latest incidents in the Bay of Piran are in violation of the Brijuni Declaration between the governments of Slovenia and Croatia on the avoidance of incidents."
Slovenes refer to the Bay of Savudrija as the Bay of Piran.
Slovene media said on Thursday afternoon that an incident had occurred in the Bay of Piran because Croatian police checked an Austrian yacht "in Slovene waters".
Slovene news agency STA said that Interior Minister Dragutin Mate addressed the Slovene parliamentary Committee on the Supervision of Secret Services on the matter on Friday and that he expected to discuss the issue with newly-appointed Croatian Interior Minister Ivica Kirin as soon as possible.