Lawmakers voted to fire Foreign Minister Salahuddin Rabbani and the ministers of public works and social services, citing a failure to spend their allocated budgetary funds on time.
The dismissals come as Afghanistan is embroiled in an economic crisis and is struggling to rein in an emboldened Taliban insurgency.
"Three ministers were disqualified by parliament after failing to spend their allocated budgets," said lawmaker Abdul Rauf Inaami, the secretary of parliament's lower house.
"If the ministers do not have the capacity to spend their budget they do not deserve to have their jobs."
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Fourteen other ministers are expected to face a similar vote of confidence, which risks tipping the government into a political crisis.
The development adds to the troubles of Ghani's government, which is already marred by infighting since the fraud-tainted presidential election in 2014.
Former rivals Ghani and Chief Executive Abdullah Abdullah have since presided over a fragile US-brokered power-sharing agreement despite their openly bitter divisions.
Abdullah, a former anti-Soviet fighter, has publicly accused Ghani of monopolising power and not consulting him over key government appointments.
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