Atta Mohammad Noor, 54, had been governor of Balkh province since 2004 but had recently been critical of the National Unity Government led by Ghani.
Noor has previously hinted that he may run for the presidency in an election in 2019. Ghani has not yet confirmed if he will run again.
The president's office in a statement said Noor, a senior leader of the Tajik-dominated Jamiat-e Islami party, had resigned from his post.
Noor was not immediately available to comment.
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But Jamiat-e Islami in a statement strongly condemned what it called a "decision by the presidency", branding it "hasty, irresponsible, against the security... and in contradiction of the principles of the National Unity Government".
It said Jamiat would announce its "clear position" on the move once its leader Saluddin Rabbani, who is also foreign minister, returns from an official trip. He is currently in Greece.
Earlier this year Noor met Deputy Chief Executive Mohammad Mohaqiq, a senior figure in the mainly Shiite Hazara ethnic community, as well as Dostum in Turkey to form the "Coalition for the Salvation of Afghanistan".