But even regional and tribal rifts began to split the Army, particularly between those of the Yoruba and Igbo tribes — a long-standing split in Nigerian society as a whole. Major General Jack Gowon, now leading the military government, sought to make provisions for a rapid return to civilian rule, but regional disputes intervened. The Igbo-dominated Eastern region sought concessions before agreeing to join the reconstituted nation. Months of diplomacy followed, with the military rulers eventually making numerous concessions to the East and its leader, Lt. Col. Chukwuemeka Odumegwu Ojukwu. On May 30, 1967, the Eastern legislature and Ojukwu declared the independent Republic of Biafra. Nigeria was at war with itself.

Both sides registered military successes in the early days of the war, but eventually the greater numbers of the Gowon government began to prevail. The Biafrans, however, won a pyrrhic victory in the propaganda war, exposing the plight of its people — starvation and mass deprivation were rampant — as well as the brutality of the federal forces. The U.S. remained neutral in the conflict, but numerous European states supported the rebels. A Swedish count actually flew combat missions for Biafra. Numerous African states recognized Biafran independence, but its legitimacy in the eyes of most Africans was compromised by the recognition granted by apartheid South Africa.