NEW DELHI (REUTERS) - India's leading crime-fighting agency registered a case on Wednesday against a prominent critic of the prime minister for accepting foreign funds, amid concerns that overseas charities are interfering in the country's domestic affairs.

An official at the Central Bureau of Investigation said Teesta Setalvad faces charges of fraud, misappropriation of funds and violation of the Foreign Contribution Regulation Act.

She did not respond to a request for comment.

A home ministry official said an investigation by government auditors revealed her non-governmental organisation, Sabrang Trust, was accepting funds from the US-based Ford Foundation without government permission.

"The NGO was cheating the government and even the donors," said a senior home ministry official, requesting anonymity.

Since the start of the year, India's government has cancelled the registration of nearly 9,000 charities for failing to declare details of donations from overseas.

Earlier this year, the Ford Foundation, one of the world's largest charitable funds, was put on a watch list after the home ministry said it was investigating the funding to Setalvad's group.

A spokesperson for the Ford Foundation did not immediately respond to a request for comment.

Critics have argued that the government's crackdown is an attempt to stifle the voices of those who oppose Modi's agenda.

Setalvad has pursued legal cases against Modi accusing him of failing to stop anti-Muslim rioting in 2002 when at least 1,000 people died in attacks on his watch as chief minister of Gujarat. Modi denies the accusations.

In a separate case, Gujarat police accuse Setalvad of embezzling funds intended to build a museum for the victims of the Gujarat riots. Setalvad denies the allegations.