The meeting assumes significance as registration of one of the Indian NGOs, Public Health Foundation of India (PHFI), which has been working in the field of public health, was cancelled by the home ministry in April.
The Gates Foundation was one of the donors to this NGO.
The home minister met Gates, co-chair and trustee of the Bill and Melinda Gates Foundation, here, an official statement said.
Singh appreciated the various welfare works being undertaken by the Bill and Melinda Gates Foundation in India and he requested Gates to initiate health awareness programmes in India.
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Assuring constructive support to India, Gates also explained about the various technologies being adopted by them in the field of agriculture and sanitation, it said.
Asked whether the issue related to cancellation of licence to the PHFI came up during the discussion, a spokesperson of the Gates Foundation said in reply to a text message that "nothing of that sort was discussed".
In an email statement, the spokesperson said Gates' meeting with the home minister focused on the progress made in the partnership with the government across the foundation's priority focus areas health, urban sanitation, digital financial inclusion and agricultural development.
After the cancellation of the FCRA registration in April, the NGO was barred from receiving foreign funds.
As per the government rules, an organisation that intends to receive foreign funds must have registration under the Foreign Contribution Regulation Act.
The action against the PHFI was taken after the home ministry found that the NGO was allegedly violating provisions of the FCRA by "diverting" foreign funds for purposes other than intended for, another official said.
According to the PHFI website, the NGO was launched by the then Prime Minister Manmohan Singh in 2006.
The NGO claimed that the governments of Gujarat, Telangana, Odisha, Meghalaya, Karnataka and Delhi are its supporters, besides Bill and Melinda Gates Foundation and other such bodies.
According to the PHFI website, they include Infosys Foundation, HT Parekh Foundation, HCL Corporation, Rohini Nilekani, Reliance Industries, GMR Projects Pvt. Ltd.
The PHFI claimed that the chairman of the executive committee of its governing body is Infosys founder N R Narayana Murthy.