After 1994, Prunk withdrew from politics for over a decade. Before the parliamentary elections of 2004, he campaigned for the Slovenian Democratic Party. In 2005, he was appointed by the Foreign Minister Dimitrij Rupel, as president of the Slovene-Croatian Historical Commission, formed by the Government of the two countries, to shed light on the history of the relations between them. Between 2004 and 2008, he served as chairman of the Slovenian Democratic Party's internal Committee for Education Policies. He resigned in 2008 because of disagreements over the Government's policy favoring private universities. After the split with the party, he became very critical of the then Prime Minister Janez Janša, whom he accused of being a "liberal with an authoritative touch, who aspires at becoming a Slovenian Piłsudski".