The interior and defence ministers were criticized for failing to prevent cross-border shelling from Pakistan and security lapses that resulted in the assassinations of senior officials.
They have also been questioned by MPs over allegations of corruption.
The vote is a blow to President Hamid Karzai’s administration, observers say.
Hamid Karzai’s office said he would make a decision on Sunday about the future of Interior Minister Besmillah Mohammadi and Defence Minister Abdul Rahim Wardak.
The president has the power to keep them in their posts for another month. In the past, he has retained his ministers for even longer.
Speaking ahead of the vote, Rahim Wardak said he had responded to cross-border attacks by sending more troops to the north-eastern border, and had deployed long-range artillery and ammunition.
But parliament passed a measure to remove him by a vote of 146 to 72.
A separate vote of no-confidence in Besmillah Mohammadi was passed by 126 to 90.
The international community appears to have lost two key Afghan figures with whom they have been dealing the most at what is a critical time.
NATO-led forces are looking to withdraw from the country by the end of 2014.
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