Special CBI Judge Vinod Kumar sent accused Anand Joshi, under secretary in the Home Ministry, to 14-day judicial remand after he was produced before the court on expiry of his CBI custody.
In its application before the court, the CBI submitted that the accused be sent to jail as he was no more required for further questioning in the case.
The court also allowed the counsel for the accused to get a copy of the FIR in the case.
Earlier, the special court had extended the CBI custody of Joshi after the agency mentioned that seven new files have been recovered during the probe.
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Joshi, who was arrested from west Delhi on May 15, was under CBI custody which ended today.
CBI had earlier claimed that the files relating to several NGOs had gone missing from Home Ministry and they were recovered from his house although he was not supposed to take them away.
It had alleged that Joshi had been issuing notices dishonestly to a large number of NGOs/societies registered under the FCRA (Foreign Contribution Regulation Act) 2010, which have been receiving significant amount of foreign contributions, in an arbitrary manner.
unconvincing answers to the questions posed by a team of Special Crime division of the CBI, including those related to disappearance of files on Sabrang Trust of activist Teesta Setalvad.
Joshi, who had disappeared from his home in Indirapuram in Ghaziabad, was picked up from Tilak Nagar area of West Delhi and taken to the CBI headquarters for questioning.
Subsequently, he was arrested by the agency.
Joshi has rejected the charge and instead accused his seniors of pressuring him to give a clean chit to NGOs. In a note which he had left before leaving home, Joshi claimed he had been subjected to "mental harassment" in recent months.
It alleged even after his transfer from FCRA division, he continued to indulge in corrupt activities on the basis of documents which were in his possession unauthorisedly.
The agency claimed that during the search conducted at Joshi's house, one file pertaining to FCRA about private NGO Care India Solutions for Sustainable Development has been seized and his interrogation was needed to know as to how the official files made way in his house and what was his intention in bringing them.
It was noticed that the files had gone missing when the Home Ministry took a decision to cancel FCRA registration of one of Setalvad's NGOs, Sabrang Trust, sources had said.