The rivalry between the IJA and IJN wasn't really an issue when it came to repatriation of overseas Japanese troops. Originally there were separate demobilization ministries for the army and navy, but it was shortly merged into a single Demobilization Bureau under the Welfare Ministry. At least for the US, Japanese army and navy prisoners of war were housed in the same camps and they were returned based on a number assigned as to when they entered the camp regardless of branch or unit.

The Japanese government was responsible for the repatriation of the approximately six million Japanese soldiers, sailors, and civilians overseas as well as the 1.5 million Koreans, Taiwanese, Chinese, and Pacific islanders in Japan although they did receive a lot of help from SCAP GHQ, which also coordinated and directed the effort.

The first issue was availability of shipping. There were eventually about 160 Japanese ships available for repatriation including merchant ships, hospital ships, destroyers, cruisers, and the aircraft carrier Katsuragi. At the time of surrender, most of these were in desperate need of repair and refitting to be able to undertake repatriation missions. GHQ G3 was in charge of repairing the merchant fleet, and the US Fifth Fleet was in charge of repairing the naval ships. The US also had to supply most of the oil for the initial voyages. Eventually the US would loan over 200 Liberty Ships and LSTs to aid in the effort, although for several months after the war ended these were needed to return US troops to the States.

The first troops that were repatriated were from the closest islands as well as from the US controlled Philippines. Repatriation would continue for several years with the last troops being returned from the Soviet Union which stretched into 1949. The Soviets had held onto Japanese prisoners for both labor and indoctrination. Most of the troops returning in the summer of 1949 sang communist songs as they left the ships, ignored their families and became involved in the Communist Party. According to the Soviets, 46,000 Japanese were buried in Siberia, but there were an additional 300,000 Japanese in Soviet controlled territory unaccounted for.

Disease was also an issue, as some returning troops suffered from smallpox, typhus, and cholera. Quarantines on the continent were not uncommon prior to repatriation. In addition to the Soviets, the Dutch and the British in Burma and Malaya held onto some prisoners for labor for nearly a year. Many Japanese POWs in the Philippines also gave fake names when they were captured, often choosing very common names which became a problem when the numerous war crime accusations began pouring in from the civilian population. A number of prisoners spent several extra months in camps as this was sorted out.

Returning Japanese troops disembarked at whatever port the repatriation ship was destined for, and would spend a few days at a demobilization center, housed in barracks or old warehouses before being given money and food to return home.