By Nita Bhalla

NEW DELHI, Sept 5 (Thomson Reuters Foundation) - The head of the Indian operations of the U.S.-based Ford Foundation, one of the world's largest charitable funds, has announced she is moving roles, hinting at discord between the organisation and the government over its handling of charities.

The foundation has had its funding frozen after the government announced a probe into a $250,000 grant it had given to a vocal critic of Prime Minister Narendra Modi.

Since Modi's right-wing government swept to power, it has sought to tighten surveillance on foreign-funded charities, saying some have not disclosed details of their donations or used overseas money to engage in "anti-national" activities.

The home ministry has cancelled the foreign-funding licenses of more than 13,000 organisations since April including Greenpeace India. Charities say the move aims to muzzle criticism of initiatives such as industrial projects affecting the poor and the environment.

In a message to the foundation's grantees, Kavita Ramdas said she had completed her three-year term as the foundation's representative to India, Nepal and Sri Lanka, and was moving to a more senior post within the organisation in New York.

But she also alluded to the current challenges faced in India, saying civil society in India had faced a "rapidly changing context and new challenges" over the past year.

"The foundation has sought to navigate these times by maintaining a direct, constructive, and ongoing engagement with the Indian government," said Ramdas in a message sent this week and provided by the Ford Foundation in New York late on Friday.

She said the foundation had recently submitted an application to be registered in "keeping with the requirements of other philanthropic organizations".

"We continue to work hard to resolve these matters, and look forward to renewing our work with committed partners across all sectors to advance the aspirations of a new generation," she said.

The Ford Foundation, which has donated more than $500 million to India since 1952, provides grants to organisations working in areas ranging from child marriage and women's empowerment to the provision of clean water in slums.

In April, the home ministry put the $12.5 billion Ford Foundation on a watch list over funding it gave to Sabrang Communications and Publishing which is run by activist Teesta Setalvad and works on conflict resolution between communities.

At the time, Setalvad was pursuing legal cases against Modi, accusing him of failing to stop anti-Muslim rioting that killed at least 1,000 people when he was chief minister of Gujarat.

Modi has denied the charges and was exonerated in 2012 in a Supreme Court inquiry.

Setalvad herself is facing charges of criminal conspiracy for illegal acceptance of foreign contribution without registration and prior permission of the home ministry.

A statement from the Ford Foundation in New York confirmed Ramdas' departure from India to work as senior advisor to the president, adding the foundation's Indonesia representative David Hulse will temporarily serve as India head. (Reporting by Nita Bhalla, Editing by Belinda Goldsmith )