Anand Joshi was placed under arrest by the CBI after he allegedly gave unconvincing answers to the questions posed by a team of Special Crime division of the CBI, including those related to disappearance of files related to Sabrang Trust of activist Teesta Setalvad.
"The official has been arrested," CBI Spokesperson Devpreet Singh said.
Earlier, Joshi, who had disappeared on Wednesday morning from his home in Indrapuram in Ghaziabad, was picked up from Tilak Nagar area of West Delhi and taken to the CBI headquarters for questioning.
"He was brought to CBI headquarter and was placed under arrest after being questioned about the allegations against him," she said.
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The case was slapped against Joshi and some other unnamed persons for allegedly indulging in corrupt practices and arbitrarily issuing notices to several NGOs, registered under Foreign Contribution Regulation Act (FCRA), which were receiving foreign contributions, including activist Teesta Setalvad's Sabrang Trust.
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 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 said.
Sabrang Trust's licence was suspended on September 9, 2015 by MHA for alleged multiple violations of FCRA rules, including misuse of funds for personal benefit of trustees.
When Home Ministry officials found that the files had gone missing, they conducted an inquiry and identified Joshi as the official who had taken away the files. He was summoned and the files were restored.