Japan ended its mission in the city of Samawa earlier this week when the security of the southern province of al-Muthanna was handed over to the Iraqi forces.
The troops had been carrying out reconstruction and humanitarian work in the province.
The Japanese were part of a multinational force in al-Muthanna that was led by the British.
The soldiers left Kuwait on a chartered flight, the Kyodo news agency reported.
The rest of the 600-strong force is expected to return to Japan in about a week.
Tokyo is not completely withdrawing from Iraq. Government officials have said Japan plans to expand its Kuwait-based air operations to take United Nations and multinational forces personnel and supplies there.
Japan's willingness to put "boots on the ground" for its ally the United States, has won praise from Washington.
The deployment was opposed by many at home including some critics who said it violated Japan's pacifist constitution.