After serving his compulsory military service as a Radioman on board the Soviet cruiser Molotov between 1949 and 1952, he was trained at the Caspian Maritime College in Baku, and commissioned as an officer in the Soviet Navy, becoming Captain 1st Rank, and in 1970 commander of the Pacific Fleet Navaga-class ballistic missile submarine К-415, with which he conducted, from January to March 1972, a trans-Pacific submerged circumnavigation.

He served as Chief of Logistics of the Far East Fleet from 1985 till retirement in 1989[1] After Georgia's independence in 1991, Javakhishvili became a commander of the embryonic Georgian navy.

With the outbreak of hostilities in Abkhazia, he personally led a successful rescue operation of Georgian civilians trapped in the Abkhaz-controlled resort town of Pitsunda on August 18, 1992.

In November 1996, he was fired for "failing to eradicate financial irregularites and raise the combat efficiency of the service", accusations which Javakhishvili rejected.

He gave an interview to the Georgian service of the RFE/RL in 2008, critical of Georgia's decision to merge the navy with the coast guard under the Ministry of Internal Affairs.