The BNP-led alliance called the first 60-hour shutdown from October 27 and second one from November 4 to press for the restoration of the neutral caretaker government system to oversee the polls scheduled to be held by January 25, 2014.
A total of 26 people have died in violence linked to the political turmoil since October 25.
Political analysts say the ministers' resignations reflect the government's firm stance for going ahead with the plan to constitute the all-party government for election oversight even if BNP declined to join the interim administration or decided to boycott the elections.