The green body said the investigators refused to submit their request in writing but verbally confirmed that they were looking into the organisation's society status - the legal basis on which Greenpeace operates in India.
"The registered office of Greenpeace India has been inspected by authorities in Chennai who are investigating the organisation's society status.
"The move was orchestrated by those who are frustrated by Greenpeace India's resilience and are searching for new ways to shut it down," the green body said in a statement.
"Greenpeace India has turned out to be stronger than the MHA expected. As a result, bureaucrats in Delhi are searching desperately for new ways to shut us down.
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"This latest move is quite obviously a response to the High Court decision last week in which the judge allowed us to use our bank accounts. We refuse to be intimidated and we will cooperate fully with this investigation, as we have done throughout," Greenpeace India programme director Divya Raghunandan said.
"Greenpeace India is a charity, and thus should be exempt from most taxes. But the government has chosen to retrospectively remove its tax exemption on a number of items. The tax bill for the year 2012-2013 is expected to reach around Rs 3 crore, which would represent most of Greenpeace India's operational budget for the next few months.
"The effect of this, therefore, would be similar to the government's previous attempt to freeze Greenpeace India's domestic accounts," the statement said.