Prime Minister Narendra Modi's nationalist government has tightened scrutiny of non-profit groups over the past four years. It says they often act against India's interests and has revoked licenses for thousands of foreign-funded groups.
Known for its campaigns against India's coal-fired power plants, Greenpeace has been barred from receiving foreign donations since 2015.
The Enforcement Directorate, India's financial crime investigating agency, froze its main bank account on Oct. 5.
"There are multi-pronged attacks on us," said Greenpeace spokesman Nandikesh Sivalingam, blaming the coal lobby.
"The coal industry is strong and powerful even if governments do want to move away from coal, including for climate change reasons."
It was not immediately possible to contact the Enforcement Directorate and a spokesman for the Finance Ministry, under which it operates, declined comment.
"I don't understand this opposition to coal," he told Reuters. "Renewable power can't take over coal for many, many years. Fortunately, we have got good coal reserves and we should use them."
Since Modi took office in 2014, India has cancelled the registration of nearly 15,000 non-governmental groups under the Foreign Contribution Regulation Act.
Critics say the government has been using the foreign funding law as a tool to silence non-profit groups which have raised concerns about the social costs of India's rapid economic development or questioned its human rights record.
In October, Indian authorities froze the bank accounts of rights watchdog Amnesty International after a raid on its office. Amnesty regularly accuses India of violations in the restive Himalayan region of Kashmir.
(With inputs from agencies.)