In January 1962 Engen was appointed commander of Carrier Air Group 11 and from early 1963 he served as operations officer on the . In April 1964, he received his first command as captain of the . He would command the ship until 31 August 1965 when he left to attend the Naval War College, in preparation for taking command of . On 21 July 1966, Engen became Captain of USS "America". During this command the USS "Liberty" incident took place and "America" launched aircraft to engage the attackers before being ordered to recall the aircraft. In July 1967, Engen passed command of "America" in Valletta and he returned to the US.