The aim of the paper is to analyse higher education institutions (HEIs) status within the state public administration system and the recent challenges in HEIs governance in Europe, Latvia, and Finland. The author uses terms "higher education institution" and "university". Higher education institutions mean public HEIs - universities, academies, and other HEIs. University is not so broad term as HEI, and it is used when describing the university role or functions. Public HEIs are part of the state public administration system, at the same time public HEIs are autonomous education and science institutions with self-government rights. On the part of state government, HEIs are brought under strict regulations; however due to their status of autonomy and self-governance, they obtain certain flexibility - there is a space for new governance processes. In the increasingly competitive higher education market, institutions shall ensure that they are responding to the demands and needs of society as best as they can. The current economic crisis is again bringing up the issue on higher education reforms. The higher education reforms are actively implemented in Finland, while the possible reforms are only discussed in Latvia. The reforms will present some new challenges also in university governance. Research object: public higher education institutions. Research subject: HEIs' status and new challenges for governance. Research basis: scientific articles, research papers, and professional literature. Research methods: monographic method and comparative analysis. Conclusions: the author comes up with several conclusions, where part of them originate from the European University Association's (EUA) recommendations to the European HEIs governance challenges.