Former editor Paranjoy Guha Thakurta took the step while keeping the office-bearers of the trust in the dark, Sameeksha Trust said in a statement.
In response, Guha Thakurta said the trustees were not sharing the "full picture" that led to his resignation.
The EPW articles claimed favours were given to the Adani Group by the Centre and that it evaded taxes. Last month, Adani served a legal notice on Sameeksha, Guha Thakurta and three co-authors of the articles, threatening legal action against them. The articles have since been taken down from the EPW website.
"The legal reply (sent on the instruction of Mr Guha Thakurta) falsely began with a statement that it was at the instruction of the Sameeksha Trust. This reply and the legal notice were placed on the EPW website, even before the Chairman and Managing Trustee were informed, so that the Trustees were completely unaware of these developments," the statement said.
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"Thereupon, Mr Guha Thakurta submitted his resignation. It was accepted by the Trustees after due deliberation," it said.
Guha Thakurta told PTI that the statement issued by the trust about the interaction that the trustees had with him on July 18 "does not give the full picture of what transpired" that day.
He said that he had acknowledged his "procedural lapse" of unilaterally taking the legal route, and had also apologised to the trust for the same.
The Sameeksha statement said EPW is a unique institution with a reputation for independent and impartial journalism, built over five decades.
Sameeksha Trust, an independent non-partisan institution, publishes research-based academic articles and evidence-based public policy critiques, providing analysis and independent commentary on topical issues.