About 220 soldiers arrived in Kuwait on military transport planes.
A total of 600 non-combat troops had been working on reconstruction projects in southern Iraq since February 2004, protected by UK and Australian forces.
The decision was unpopular with the Japanese public, many of whom said it violated Japan’s pacifist constitution.
“Our ground forces have bravely completed their mission and have now safely withdrawn to Kuwait,” Japanese Prime Minister Junichiro Koizumi told reporters in Russia, after the G8 summit.
“We carried out our humanitarian and reconstruction tasks without firing a single shot – in fact, without pointing a gun at anyone.”
The soldiers were greeted in Kuwait by Japan’s defence chief Fukushiro Nukaga. They are due to return to Japan in about a week, according to the Associated Press.