Masooma Muradi had faced strong resistance from religious conservatives and political opponents since her appointment in 2015 as governor of Daikundi, a remote province in central Afghanistan.
"I can confirm Masooma Muradi, the governor of Daikundi, has been replaced," Munera Yousufzada, a spokesperson for the directorate of local governance, told AFP without giving a reason.
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"This is a normal procedure in the government. We are thankful for all her efforts. This is not any kind of prejudice against women." Yousufzada said Muradi had not been assigned another job.
Muradi was handpicked by President Ashraf Ghani to lead Daikundi, but protests erupted even before she arrived in the impoverished province as her male political opponents attacked her lack of experience.
Her ascent to the post was a remarkable feat in Afghanistan where stubborn patriarchal traditions and conservative attitudes about a woman's place in the world persist.
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Despite Ghani's efforts to appoint women to senior positions, Afghan politics remains largely a man's domain with just a handful of women holding down political positions.
In the entire country there are just two female ministers - counter-narcotics and women's affairs - one female deputy governor and two women district governors.
Ghani dismissed the only other woman governor, of central Ghor province, after protests from religious conservatives.
Muradi, who holds a degree in business administration, was a stark contrast to the warlords and strongmen who govern other provinces under a deep-rooted system of patronage politics.
In an interview with AFP last year Muradi said many people could not "bear having a woman in this position".
"I won't allow men to hush me up - society is not used to that from a woman," she said.
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