The Central Bureau of Investigation on Friday raided the residence and office of an undersecretary posted with the Ministry of Home Affairs (MHA), a top government official told The Hindu.

The raid comes months after files pertaining to the alleged Foreign Contribution Regulation Act (FCRA) violations by social activist Teesta Setalvad’s two NGOs went missing from the Home Ministry. The files were traced and restored in the FCRA division but the CBI was asked to investigate the matter.

Officials noticed the files had gone missing when they wanted to take a decision to cancel the FCRA registration of one of her NGOs, Sabrang Trust.

Sabrang Trust’s licence was suspended on September 9, 2015 by the MHA and it asked the firm for an explanation, failing which the FCRA registration would have been cancelled in 180 days. Ms. Setalvad filed her reply in October itself and the deadline given by the MHA expired in March this year.

“It is at this point of time we realised the files had gone missing. We conducted an inquiry and identified the official who had walked away with the files. He was summoned and the files were restored,” said a senior government official.

Ms. Setalvad pursued the Gujarat riots case of 2002 when Prime Minister Narendra Modi was the State’s Chief Minister.

Soon after the NDA government came to power, based on a report sent by the Gujarat government, the MHA took series of actions against the NGOs and organisations associated with Ms. Setalvad.

In 2015, the MHA put another of Ms. Setalvad’s NGO, the Citizens for Justice and Peace (CJP), under the “prior permission category.”

The CBI is also probing a case against Ms. Setalvad on the MHA’s complaint.

“The CBI was roped in as there could be other cases where the concerned official would have misplaced files.

The motive is not clear yet. The CBI is doing its investigations,” said the official. No arrests have been made so far. The Home Ministry has already set up a one-man inquiry commission to trace certain file notings related to Ishrat Jehan fake encounter case, which have gone missing.