"I reject those allegations. We carried out that mission professionally and with as few casualties as possible," Lisjak said in an interview with the commercial television network POP-TV on Friday.
Lisjak commanded the Slovene Territorial Defence forces in operations around the Rozna Dolina crossing near Nova Gorica on the border with Italy.
Lisjak said he had been ordered to take control of the border crossing which the Yugoslav People's Army (JNA) occupied on 27 June 1991 after Slovenia declared independence from Yugoslavia.
According to him, 180 JNA personnel and only nine Slovene soldiers were involved in the fighting there.
Lisjak was commenting on the allegations by Josip Birkic from Croatia, who has said that members of the Slovene Territorial Defence fired at JNA conscripts even after they got out of their tanks to surrender. Birkic was doing his national service in the JNA at the time.
Asked to comment on reported violations of the laws of war by Slovene forces near the border crossings of Holmec and Rozna Dolina in 1991, Lisjak said that those reports were attempts by Croatia and Serbia to join the European Union by shifting the blame for the break-up of Yugoslavia onto Slovenia.