In an email to staff, Shoma Chaudhury denied being part of a "cover-up" to protect Tehelka's founder and editor Tarun Tejpal who is under investigation over claims he sexually assaulted the woman in a hotel in the holiday state of Goa.
However Chaudhury, who announced last week that Tejpal was standing aside for six months over what he has described as "a bad lapse of judgement," acknowledged that "she could have done many things differently."
The alleged victim, who has since resigned from the magazine, first made the allegations against Tejpal in a detailed email to Chaudhury.
"As a result of what's transpired over the past few days my integrity has repeatedly been questioned by people from our fraternity and, in fact, by the public at large," Chaudhury wrote in her mail which has been seen by AFP.
"I do not want questions raised about my integrity to tarnish the image of Tehelka, which it has done in the past week. Therefore, I resign as Managing Editor with immediate effect," she added.
Chaudhury's resignation comes three days after the alleged victim also quit the magazine, saying she had come under pressure from Tejpal's family to drop her allegations.
Tejpal, 50, is due to be questioned by Goa police later Thursday.
Tehelka has garnered a reputation for hard-hitting investigations on corruption as well as sexual violence against women and gender inequality, and was hailed for its reporting of a deadly gang-rape in New Delhi last December.
The Tehelka scandal has dominated the Indian news agenda for the last week, with rivals accusing the magazine of hypocrisy.
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@romm: only tehelka ,and we know who is funding tehelka.
it speaks High moral standards of Indian media, however, people like Amir Liaqat are reemployed by leading media groups.