Women's affairs minister Husn Bano Ghazanfar was the thirteenth of 24 candidates who failed to win approval, when she fell two votes short of the total needed for confirmation.
The justice, commerce, energy, economy, public health and communications portfolios were among posts left empty after parliamentarians made use of a rare opportunity to flex their political muscle.
At a time when Afghanistan's security and corruption problems are worsening, parliamentarians have been exercising their influence, quizzing potential ministers over the past week on former policy and future plans.
Reuters quotes Fowzia Kofi, Afghan Member of Parliament, as saying that "the government of Afghanistan is facing very big problems such as poverty, corruption and insecurity. I hope that our security sector especially those ministers who received the vote of confidence rethink the security situation in the country".
The Parliament is reported to have remained in session for at least three extra hours to complete the voting procedure because of a complicated secret ballot process.
Meanwhile, two rockets are reported to have been fired in Afghanistan's Helmand district during President Karzai's visit to the region.
Witnesses said explosions were heard around two hundred meters away from the platform where Karzai was addressing an audience of some five hundred people.
No casualties have been reported.