A group of Afghan nationals who worked for the Japanese embassy and the Japan International Cooperation Agency's office in Afghanistan arrived in Japan with their families on Friday.
Tokyo worked with the Qatari government, which has a relationship with Afghanistan's ruling Islamist group, the Taliban, to get them out of the country.
The 53 people flew to Qatar on a civilian airplane earlier this month.
It was the first time the Japanese government has used a civilian plane to evacuate local staff.
No health issue has been found with the people who arrived in Japan.