At a 1966 Lahore conference of both the eastern and the western chapters of the Awami League, Mujib announced six-point political and economic program for East Pakistani provincial autonomy. He demanded that the government be federal and parliamentary in nature, its members to be elected by universal adult suffrage with legislative representation on the basis of population; that the federal government have principal responsibility for foreign affairs and defense only; that each wing have its own currency and separate fiscal accounts; that taxation would occur at the provincial level, with a federal government funded by constitutionally guaranteed grants; that each federal unit could control its own earning of foreign exchange; and that each unit could raise its own militia or paramilitary forces.

Mujib's six points ran directly counter to President Ayub's plan for greater national integration. Ayub's anxieties were shared by many West Pakistanis, who feared that Mujib's plan would divide Pakistan by encouraging ethnic and linguistic cleavages in West Pakistan, and would leave East Pakistan, with its Bengali ethnic and linguistic unity, by far the most populous and powerful of the federating units. Ayub interpreted Mujib's demands as tantamount to a call for independence. After pro-Mujib supporters rioted in a general strike in Dhaka, the government arrested Mujib in January 1968.             

In January 1968, Sheikh Mujib and 34 Bengali civil and military officials were arrested on charges of their involvement in the so-called Agartala conspiracy to declare independence of East Pakistan. Their trial proved the charges hollow and the case had to be withdrawn by February 1969 under angry protests by the Bengalis.