Four years later, when the Spanish Civil War started, he was in command of the military tugboat Cíclope (RA-1)[3] and refused to join the July 1936 pro-Fascist coup, remaining loyal to the republic.

His brother Francisco, a commander of the Spanish Republican Army, joined the rebel faction after the coup and was killed in action in the front near Madrid early in the Civil War.

[5] In the dire 1936 post-coup reorganization of the Spanish Republican Armed Forces, Prieto did away with the Navy 'ship committees' and sought to create a structure that would reimpose discipline after the bulk of the top commanders had defected to the rebels.

[8] Shortly thereafter, on 5 March 1939, Spanish Republican Army Colonel Segismundo Casado launched an anticommunist coup and proclaimed a National Defence Council (Consejo Nacional de Defensa) in order to seek an armistice with the rebels and end the fratricidal war, a measure that Miguel Buiza favored.

On the same day, the Nationalist Air Force bombed the harbour of Cartagena, the main base of the Republican Navy, sinking the destroyer Sanchez Barcaiztegui.

[9] Following the bombing and the unrest in the city, where a rebellion was under way between adversaries and supporters of the continuation of the civil war,[10] Miguel Buiza decided to evacuate the seaworthy units of the Republican fleet.

[11] Except for a few crewmen who were put on guard duty on the ships, the Spanish Republican seamen and their officers were interned in a concentration camp at Meheri Zabbens, near Meknassy, in an abandoned phosphate mine.