In Sudan, internal conflict between the government and rebel groups in the southern part of the country lasted for more than 20 years from the 1980s, finally ending with the signing of a peace agreement in January 2005. Soon thereafter, in March 2005, the United Nations decided to establish the United Nations Mission in Sudan (UNMIS). Japan dispatched two staff officers to the mission. With the independence of South Sudan in Jully 2011, UNMIS ceased its operation.

Even after the conflict, however, the Office of the United Nations High Commissioner for Refugees (UNHCR) and other agencies have continued providing relief supplies on the ground.