Immigration officials stamped "offload" on Priya Pillai's passport.
Ms Pillai, who says she had a valid visa for the UK, was to talk to law-makers there about why Greenpeace believes a proposed coal mining project, planned for Mahan in Madhya Pradesh, would hurt the area's forest community.
The Ministry of External Affairs said it has no say in immigration clearance.
The Home Ministry refused to comment on record. Speaking on condition of anonymity, senior officials told NDTV that Ms Pillai is on a list of people who are meant to be stopped by airport officials from leaving or entering the country, because they have been red-flagged by a government agency or state police. "The government is well within its rights to prevent individuals from leaving the country, if it believes that it is against interest of the country," a senior official said.
Ms Pillai said yesterday that she was charged with trespassing after participating in a protest in Mahan. Today, she tweeted that she has no clarity on who stopped her travel.
In June, the government tightened controls on foreign fund transfers to Greenpeace India after an intelligence report accused activist groups of "stalling development projects" by protesting against power and mining projects. The report alleges that Western countries were using activist groups in India to promote their foreign policy goals.
Four months ago, a British Greenpeace staff member was stopped from entering India and put back on a London-bound flight.
Greenpeace says that though the Delhi High Court directed authorities in September, 2014, to unblock its accounts, it has not received any money since then.
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