The national Investigative Bureau's report - a copy of which was obtained Thursday by the Associated Press - also accuses the groups including Greenpeace, Amnesty International and Action Aid of providing reports ''used to build a record against India and serve as tools for the strategic foreign policy interests of Western Governments.''
The Home Ministry said Thursday it would neither confirm nor deny the existence of the report, which has sparked a firestorm of debate in Indian newspapers and on TV news channels.
But in a letter last week, the ministry ordered the Reserve Bank of India to hold all foreign contributions to India-based charities until they are cleared by the ministry, spokesman K.S. Dhatwalia said. He said Thursday the order would help the government control how much money was coming into India, and how it was being spent. The charities had previously reported annually on how they used their funding.
The report specifically criticized the charities for organizing public protests against nuclear power plants, uranium mines, coal-fired power plants, genetically modified crops and electronic waste.
''The negative impact on GDP growth is assessed to be 2-3 percent'' each year, the report says, without elaborating on how that assessment was made.
Organizations and activists named in the report called the allegations ludicrous.
''If indeed we are a threat to national security, one would assume the government would move to engage with us,'' Greenpeace India's executive director, Samit Aich, said in a written statement to AP. ''This seems to be a slander campaign designed to pave the way for rash (project) clearances, high-handed action against civil society and corporate Raj.''
The crackdown reflects India's struggle to balance industrial and economic development with protecting and elevating its staggering number of poor.
While rapid economic growth - averaging near 10 percent for the past decade - has boosted the incomes and living standards of millions, a two-year downturn with GDP growth falling below 5 percent has made many nervous. Inflation has rocketed into double digits, and job growth has stalled.
Demands for economic revival helped catapult Prime Minister Narendra Modi and his Bharatiya Janata Party to a landslide election victory in May. Some have blamed public resistance to development projects for holding up economic growth.
But many of the country's 400 million impoverished - earning less than $1.25 a day and relying heavily on foraging for food, fresh water or firewood - have become anxious about environment degradation. Indians breathe some of the world's dirtiest air, bathe in toxic or fetid rivers and face extreme water scarcity within a few years.
The Intelligence Bureau submitted its report - titled ''Concerted efforts by select foreign funded NGOs to `take down' Indian development projects'' - to the national government on June 3, just days after Modi's government took over.
Greenpeace, it says, was specifically campaigning against e-waste disposal ''in order to undermine the image'' of India's IT firms. It says, however, that the campaign failed to achieve its goal of ''eroding the earnings of the IT firms.''
Greenpeace called the allegations baseless, and said no one in the organization had been contacted by the report's investigators. It says its Indian chapter receives 61 percent of its money from Indian donors and 39 percent from Greenpeace International.
''If they had taken us on board, they would have definitely come to a different conclusion. They did not take our view,'' said the group's communication director, Bharati Sinha. Greenpeace also said the government has refused to show the organization a copy of the report.
''These tactics will not stop Greenpeace from speaking truth to power and continuing to raise issues that are essential for protecting the environment for current and future generations.''
Anti-nuclear activist S.P. Udayakumar, accused in the report of taking money from a U.S. group to organize 2011 resistance to a Russian-built nuclear power plant in the southern state of Tamil Nadu, also said the allegations were preposterous. His lawyer has notified the Home Ministry of plans to sue for defamation of Udayakumar's character unless the ministry issues a retraction.
''There is no truth in the allegation,'' he told reporters about the report, which he said was designed to harm his reputation.