Troops of northern origin, who made up the bulk of the infantry, became increasingly restive. Fighting broke out between them and Igbo soldiers in garrisons in the south. In June mobs in the northern cities, abetted by local officials, carried out a pogrom against resident Igbo, massacring several hundred people and destroying Igbo-owned property. Some northern leaders spoke seriously of secession. Many northerners feared that Ironsi intended to deprive them of power and to consolidate further an Igbo-dominated centralized state.

In July northern officers and army units staged a countercoup, during which Ironsi and a number of other Igbo officers were killed. The Muslim officers named thirty-one-year- old Lieutenant Colonel (later Major General) Yakubu "Jack" Gowon, a Christian from a small ethnic group (the Anga) in the middle belt, as a compromise candidate to head the FMG. A young and relatively obscure officer serving as army chief of staff, Gowon had not been involved in the coup, but he enjoyed wide support among northern troops who subsequently insisted that he be given a position in the ruling body. His first act was to repeal the Ironsi decree and to restore federalism, a step followed by the release of Awolowo and Enahoro from prison.