Tanzeela Mazhar had gone public with her account of harassment and unwanted advances by the official earlier this year, forcing authorities to promise a fair investigation.
But Mazhar said she resigned due to the alleged failure of the authorities to do justice in her case.
"Things were made very difficult for me to work and I was facing huge psychological torture every day," she wrote in her resignation letter, which she has shared on Twitter.
Mazhar had complained that PTV's current affairs director had "made unwelcome advances" at her in 2009 and due to her resistance she was "put off screen for [a] few months."
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"I regret that the higher management of PTV chose to save one person over the reputation of PTV. So I find it very difficult to continue working," she wrote in the letter.
Mazhar and Yashfeen Jamal were the two female anchors from PTV who had accused the official of making sexual advances.
A senior PTV producer told Dawn newspaper that three key figures, including a federal minister, wanted the alleged abuser to get a "clean chit". He said the inquiry report was amended at least six times to make it favourable to the accused, which was why it had not been finalised in time.
Members of South Asian Women in Media (SAWM) - a regional forum for women working in the media industry - had also demanded a fresh probe into the harassment allegations.
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