Chowdhury was shifted to Home Ministry in place of A K Jain, a 1977 batch IAS officer of Nagaland cadre.
Jain, who was holding the charge as the Secretary of official languages in Home Ministry, has taken charge as the new Secretary in Women and Child Development Ministry.
Chowdhary is a 1977-batch IAS officer of Uttar Pradesh cadre.
Chowdhury, who had taken over as Secretary in WCD ministry in June last year, had come under criticism after a senior official of the Ministry allegedly slit her wrist in her Shastri Bhawan office on July 23.
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The official was later transferred to a different Ministry.
Later, several others officers had also complained to the WCD Minister that they were being allegedly harassed by Chawdhury at work place, sources said.
Tirath had also recently written to the Cabinet Secretary seeking Chowdhury's transfer.