Throughout the remainder of 1966 and into 1967, the FMG [Federal Military Government] sought to convene a constituent assembly for revision of the constitution that might enable an early return to civilian rule. Nonetheless, the tempo of violence increased. In September attacks on Igbo in the north were renewed with unprecedented ferocity, stirred up by Muslim traditionalists with the connivance, Eastern Region leaders believed, of northern political leaders. The army was sharply divided along regional lines. Reports circulated that troops from the Northern Region had participated in the mayhem. The estimated number of deaths ranged as high as 30,000, although the figure was probably closer to 8,000 to 10,000. More than 1 million Igbo returned to the Eastern Region. In retaliation, some northerners were massacred in Port Harcourt and other eastern cities, and a counterexodus of non-Igbo was under way.

The Eastern Region's military governor, Lieutenant Colonel Chukwuemeka Odumegwu Ojukwu, was under pressure from Igbo officers to assert greater independence from the FMG. Indeed, the eastern military government refused to recognize Gowon's legitimacy on the ground that he was not the most senior officer in the chain of command. Some of Ojukwu's colleagues questioned whether the country could be reunited amicably after the outrages committed against the Igbo in the Northern Region. Ironically, many responsible easterners who had advocated a unitary state now called for looser ties with the other regions.

The military commanders and governors, including Ojukwu, met in Lagos to consider solutions to the regional strife. But they failed to reach a settlement, despite concessions offered by the northerners, because it proved impossible to guarantee the security of Igbo outside the Eastern Region. The military conferees reached a consensus only in the contempt they expressed for civilian politicians. Fearing for his safety, Ojukwu refused invitations to attend subsequent meetings in Lagos.