Perch recommissioned 11 November 1961, Lt. Comdr. Charles H. Hedgepeth in comand, trained on the West Coast and Hawaii through 1962 and arrived at her new homeport, Subic Bay, Philippine Islands in March 1963. Her operations consisted of training Marine, Special Forces, and UDT personnel in reconnaissance and also in providing training services to allied countries. In May and June 1964 Perch traveled to Mindoro and trained with British commando forces. July and August were spent in Honh Kong, Pohong Bay, Korea (with R.O.K. Special Forces), Yokosuka and Okinawa.
March and April 1965, saw Perch participating in exercise "Jungle Drum lll" by landing 75 Marine Corps reconaissance personnel on the Malay Peninsula from the Gulf of Siam. Perch conducted search and rescue operations in the Vietnam combat zone during August and September. She made two amphibious landings on the coast of South Vietnam during November and December.as part of opperation "Dager Thrust".
During January Perch landed UDT personnel for beac survey work in South Veitnam as part of operation "Double Eagle". She then provided services at Legaspi, P.I. to train Filipino and American UDT personnel. Between local training operations in the Subic Bay area, Perch worked with Chinese Special Forces at Kaohsiung, Taiwan, and with Army Special Forces at Keelung, Taiwan.
In July Perch participated in operation "Deck House ll" on the coast of South Vietnam. Again in August Perch conducted several independant beach surveys of South Vietnam. For Operation "Deck House lV" in September Perch
landed UDT personnel on five successive nights for preinvation beach reconnaissance.
On Octobet 7, 1966, Perch headed for Pearl Harbor via Hong Kong, Palau Islands, Guam, and Midway Island. She operated in Hawaiian waters until 1967 when she became Naval Reserve Training submarine at San Diego. On 22 August 1968, Perch's classification was changed from APSS-313 to LPSS-313. Into 1970 she continues to serve reservists.