After the Klaipėda Revolt of 1923, Merkys became secretary to the Klaipėda Region Commissioner, Antanas Smetona. Following the 1926 Lithuanian coup d'état, he became Minister of Defence again until 1927, when he was made Governor of Klaipėda Region. In 1932, German demands prompted his removal as Governor and Merkys returned to practising law. He became Mayor of Kaunas in 1933 and served in this position until 1939. In 1936 was elected to the Fourth Seimas of Lithuania. On 17 November 1939 he became Prime Minister.