On October 1 1963, CNO directed a merger between Boat Unit ONE and LCU Squadron ONE in order to combine and streamline the operation of the two similar commands. Boat Unit ONE was disestablished and all boats and personnel were transferred to the three LCU Divisions. LCU Squadron ONE was renamed Assault Craft Squadron ONE (ACS-1), and the divisions changed from LCU Divisions to Assault Craft Divisions. The Squadron Commander was classified as a Commodore, with each Division having its own Commanding Officer and organizational staff. The squadron still retained its Western Pacific Detachment. Beginning in 1963, ACS-1 craft were deployed to South Vietnam. Based at Naval Support Activity Danang, ACS-1 craft resupplied Marine forces far up river, and conducted day and night armed reconnaissance patrols. Over 20 ACS-1 Sailors were lost to hostile fire during this conflict, including the entire crew of LCU-1500. ACS-1 craft maintained a constant presence through the end of the conflict.
On 1 May 1968, CNO directed that Assault Craft Squadron ONE and its Assault Craft Divisions ELEVEN, TWELVE and THIRTEEN be disestablished, and reformed as Assault Craft Unit ONE (ACU 1). The overseas division became ACU-1 WESTPAC Detachment. The Squadron Commodore became the Commanding Officer.