Delhi Police will conduct the probe and submit its report to the Union Home Secretary, a Home Ministry official said.
The IB report, 'Impact of NGOs on Development', had been sent to the Prime Minister's Office, the Home Minister, the National Security Adviser, the Finance Minister and others.
Last month, excerpts from the report appeared in media creating an uproar.
It claimed that the NGOs work for stalling development projects along with agitations against nuclear power plants, uranium mines, coal-fired power plants and hydel projects.
"It is using foreign funds to create protest movements under 'Coal Network' umbrella at prominent coal block and coal-fired power plant locations in India," the report said.
Reacting to the charge, Greenpeace had said instead of destroying India's forests to access coal underneath, it believes India should embrace renewable energy and energy efficiency to meet rapidly-increasing energy needs.
After the IB report, the Home Ministry had issued a directive to the Reserve Bank of India asking it to put on hold all foreign contributions originating from Greenpeace International and Climate Works Foundation.
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