The war began with ethnic rivalry in the armed forces. After the military coup in January 1966, in which Tafawa Balewa's government was overthrown by junior Igbo officers, Major-General Johnson Aguiyi-Ironsi, an Igbo, was the appointed head of government by ministers that survived the January 1966 coup. Anti-Igbo riots followed with traditionalist Muslim attacks on Igbo people residing in the north, in September of 1967, which resulted in a massacre; 30,000 deaths and massive Igbo flight of over 1 million, from the north to the east. Easterners, who had previously supported the idea of a united Nigeria, now opposed it based on fear of safety outside the eastern region. The Federal Military Government (FMG) made peace offerings and invited military governor of the eastern region, Lieutenant-Colonel Chukwuemeka Odumegwu-Ojukwu to peace talks in Lagos, (the former capital located in the west), but Ojukwu rejected them.

In January, 1968, Ojukwu finally met with Gowon, some other regional leaders and police on neutral territory - Aburi, Ghana under the protection and mediation of the Ghana's military government. The agreement reached at this conference was that a loose confederation of the regions might solve Nigeria's ethnic problems. This agreement was violently opposed by civil servants in Lagos. Awolowo, the leader of the western region demanded the removal of all northern troops in the west, and threatened to leave the federation if the east did so first. The FMG subsequently removed northern troops from the west; "and issued a decree resurrecting the idea of a confederation discussed at Aburi." Ojukwu and the other eastern leaders rejected it, by voting in May to secede from Nigeria. The mid-western region, the present location of Nigeria's capital - Abuja - announced that it would remain neutral in the event of a civil war.

On May 30, 1967 Ojukwu formally announced that Biafra would be an independent Republic. He stated that Nigerian government's inability to protect the lives of easterners and its collaboration in genocide forced the Igbo to secede from the federation. In July army combat units were dispatched to the east, but were met with rebel troops. Biafrans retaliated by taking control of strategic points in the mid-western region. The FMG reacted by sending large numbers of the armed forces to fight in a full-scale civil war. The FMG regained control of the mid-west and the delta region, and terminated Biafra access to the sea by the end of 1967, yet, they were unable to penetrate the Igbo heartland - resulting in a stalemate.

Outnumbered and outgunned, the rebel troops had the advantage of excellent leadership and morale. However, the FMG invaded Owerri, an oil rich area of the Niger delta, in 1968 and increased their army to 250,000 men. The Biafran rebels liberated Owerri. However, but a new federal offensive in the south forced the rebels into submission.

Lieutenant Colonel Yakubu Gowon proclaimed a state of emergency and announced plans for abolition of the regions and the re-division of the country into twelve states. This effort was recognized as a concession to the eastern region that removed northern domination, and as a strategic move, which won over eastern minorities and deprived the rebellious Igbo heartland of its control over the oil fields and access to the sea. The division of Nigeria into 12 states took effect in April 1968 and the East Central State, formerly Biafra, was reintegrated into Nigeria after the cease-fire in January of 1970.