Compassion International is the biggest international charity working in India and sends $50 million (£40 million) in humanitarian aid to the country annually.
The charity is scheduled to withdraw from India by 15 March.
Compassion said that the Indian Government told them last year their partners on the ground had to submit a new application form in order to continue to receive funding from the charity. Sixty-three of Compassion's partners had their application forms rejected.
This meant that Compassion was no longer permitted to keep funding any of their partners in India.
In an email to supporters in January, Compassion said: "Since we can no longer distribute funds to our field offices, we have just had to notify our India country staff that we must formally close our field offices in India by March 15."
It's been claimed the Indian government banned funding for the groups because of Compassion's methods of evangelisation, with security agencies claiming that the charity is actively involved in religious conversions under the guise of social and cultural activity.
"It is part of the colonial civilising mission still continuing," Madhu Kishwar, an academic and journalist told The Guardian.
"They use health and education as outreach, but harvesting of souls is their primary activity."
The charity say that despite repeated attempts to resolve the issues with the Indian government, attempts had failed.
Compassion has worked in India for 48 years.