The Cabinet decided Tuesday to extend the Self-Defense Forces deployment in South Sudan by four months to the end of February.
The decision came after the U.N. Security Council extended the operation of the U.N. mission in South Sudan, which the SDF personnel are part of, until Nov. 30.
The final three months will be used to prepare for the troops' withdrawal, a government official said.
The plan includes the assignment of an SDF officer to the U.N. mission command, Chief Cabinet Secretary Yoshihide Suga told a news conference.
"Peace and stability in South Sudan are extremely important for the international community," he said.
Defense Minister Akinori Eto separately told reporters that "the SDF will work hard to do its part, as it's quite important to maintain security and engage in peacekeeping operations."
Japan began dispatching Ground Self-Defense Force personnel in November 2011, with about 400 troops engaged in infrastructure building at one point.
Fighting in the capital Juba forced them to suspend work last December, and they now mainly provide support at U.N. facilities for displaced people seeking refuge from violence.
Prime Minister Shinzo Abe is trying to expand the role of the SDF abroad so Japan can make "proactive" contributions to global peace and security. He is pushing for a series of security policy changes by loosening the legal constraints imposed by the pacifist Constitution.