The first batch of Japanese air personnel left earlier in the week
Japanese Prime Minister Taro Aso has praised his country's five-year non-combat mission in Iraq, as the last planes flew out of the region.
He said he was "happy and proud that the personnel completed their jobs safely and without incident".
The deployment was Japan's first to a combat zone since World War II. It sparked considerable public opposition in the officially pacifist country.
South Korea is due to end its four-year mission in Iraq on Friday.
The last of the 18,000 South Korean troops that have served in Iraq and Kuwait since 2004 were withdrawing from their current base in the northern Iraqi city of Irbil.
Mr Aso not only hailed the country's air force personnel but also their families for their support, calling them "two wheels of a cart", Kyodo news agency reports.
FOREIGN TROOPS IN IRAQ
US - Around 146,000
Britain - 4,100
Australia - 980
Romania - 397
El Salvador - 280
Estonia - 34
Figures from AFP news agency
The last three C-130 freighter planes flew out of Kuwait for Japan late on Wednesday. The majority of the 210 air force staff will have returned home from Kuwait by next week.
Japan has been contributing to the Iraqi mission since February 2004, when former Prime Minister Junichiro Koizumi sent in ground troops to help with reconstruction projects.
He withdrew the soldiers before leaving office in 2006. Members of Japan's air self-defence force have remained in Kuwait, flying goods and personnel into Iraq.
The presence of Japanese forces in Iraq has been controversial.
Some members of the ruling Liberal Democratic Party argue that Japan should be more involved in global security efforts to help the country's standing on the world stage.
But critics fear it threatens the country's pacifist constitution, which was written after the country's defeat in 1945.