The post had fallen vacant after M A Sikandar retired in August last year.
"The HRD ministry on Wednesday cleared Rita Chowdhury's name as the next Director of NBT," ministry officials said.
Chowdhry, wife of former president of Asom Gana Parishad (AGP) Chandra Mohan Patowary who joined BJP last year, is a Sahitya Akademi Award winner and a professor of political science at Cotton College, Guwahati.
The filling up of the crucial post in NBT comes amid allegations that the government was appointing persons with close links to BJP at the top level.
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In March, NBT chairman A Sethumadhavan had to step down under controversial circumstances, following which the ministry had appointed Sharma to the post.
Chowdhury's appointment as Director has also raised a few eyebrows as her husband had joined BJP last year. She was considered a front runner for the post for which ministry conducted interviews twice.
Established in 1957 with an objective of producing and encouraging quality literature in English, Hindi and other languages, the National Book Trust (NBT) works under the purview of the HRD Ministry.
The director looks after the editorial functions of 24 editors working in Indian languages.