According to the statement, Baghlan governor Farid Baseem has resigned due to personnel issues.
President Ashraf Ghani has accepted his resignation.
The statement further said that the provincial deputy governor Abdul Qadim Niazi will act as caretaker until the appointment of a new governor.
This comes after Taliban militants intensified their attacks by surrounding the province for nearly one week.
The insurgent group also blocked Kabul-Balkh and Baghlan-Kunduz highways which was reopened after Afghan forces conducted an operation.