The visit is Kouchners second trip to Iraq in less than a year. It comes as France prepares to assume the rotating EU presidency in July.
The French foreign minister said his visit was a "message of peace and cooperation" and a chance to discuss any future French contribution to rebuilding Iraq.
Kouchner arrived in the southern city of Nasiriyah from Jordan, where he announced France will try to take in about 500 Iraqi Christian refugees "because of the oppression of some Christians in Iraq."
Speaking to reporters while touring the ancient ruins of the biblical city of Ur with Shi'ite Vice President Adel Abdul-Mahdi and the governor of Dhi Qar Governorate, Aziz Kadhim Alwan, Kouchner said four Iraqi children would travel to France to undergo cardiac surgeries.
The French Foreign Ministry said Kouchner is scheduled to hold meetings with Prime Minister Nuri al-Maliki, President Jalal Talabani, and Foreign Minister Hoshyar Zebari during his two-day visit. Kouchner was also due to meet religious and civic leaders, and visit the Kurdish northern city of Arbil, where he would inaugurate a new French embassy office.
During his previous visit to Iraq in summer 2007, Kouchner said France, which had been one of the fiercest critics of the U.S.-led invasion in 2003, wanted to "turn the page" and look to the future.
Nasiriyah, about 320 kilometers southeast of Baghdad, has recently been the scene of clashes between Shi'ite militias and U.S.-Iraqi forces. The situation has calmed since anti-U.S. cleric Muqtada al-Sadr declared a truce, but sporadic violence continues.
The U.S. military said the Imam Ali base where Kouchner landed was hit by rockets or mortar shells late on May 30, but no casualties were reported.
With material from agency reports