The award is given annually by the European Commission for outstanding reporting on human rights issues.
The awards ceremony was held in Brussels, Belgium on 8 December. Naqvi's article was among 17 finalists selected from 1,300 entries.
The celebrated article India-No Country For Little Girls is a harrowing piece on an important human rights issue - India's continuing discrimination against female infants despite the country's economic growth.
John Daniszewski, AP Vice President and Senior Managing Editor for International News, said: "AP congratulates Muneeza for her extraordinary work and the award achieved."
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