The CBI is looking into whether her NGO received funding from the United States-based Ford Foundation without government permission.
She says she is being persecuted for the cases that she filed earlier against Prime Minister Narendra Modi, accusing him of failing to stop the communal riots that ravaged Gujarat in 2002. The Supreme Court has said there is no evidence that as Chief Minister at the time, Mr Modi did not do enough to stop the violence which killed at least 1,000 people.
The CBI registered the case against Ms Setalvad, 53, and her husband, Javed Anand, on July 8 and raided their home and offices a week later. At an earlier hearing, the agency controversially described her as “a threat to national security.”
Ms Setalvad has also been charged by the Gujarat police of embezzling funds donated to the non-profits she runs for victims of the Gujarat riots.
Ms Setalvad has denied any wrongdoing in the multiple cases she confronts.
The CBI says its investigation is based on a complaint from the Home Ministry and that the sum involved is over 1 crore rupees ($160,000).
Amid a crackdown on foreign charities, the Home Ministry put the $12.5 billion Ford Foundation on a watch list this year. The PM has also criticized what he called “five-star activists”.