Special CBI Judge Vinod Kumar gave the relief to Joshi, who was an under secretary in the Home Ministry, on furnishing of a personal bond of Rs 50,000 and two sureties of the like amount.
"Accusations are serious but the accused cannot be put in jail for an indefinite period. Considering that he is not likely to abscond, bail is granted to the accused," the judge said.
The court directed Joshi not to leave Ghaziabad and Delhi till the time investigation is over and also asked him to deposit his passport with the investigating officer (IO).
It, however, said that in case of any emergency, he can leave for Ranchi, where his parents reside, after taking the court's prior permission.
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"He will not try to influence any witness or to contact any of the NGOs being probed," the court said.
The court also asked Joshi to make his presence before the IO every Monday.
Joshi sought bail, saying that he was not in a condition to influence any witness or NGO and that he has been transferred from the Home Ministry.
Opposing the plea, CBI said that if granted bail, Joshi could threaten witnesses as he was in an influential capacity.
It also submitted that a large number of NGOs were required to be investigated and there were apprehensions that he could abscond.
Joshi, who was arrested from west Delhi on May 15, was presently under judicial custody.
CBI 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.
CBI had said some of these organisations were Care India, Snehalya Charitable Trust, Indian HIV/AIDS Alliance and All India Primary Teachers Federation and alleged that representatives of some of these organisations were called and Joshi had demanded and obtained illegal gratification.
Joshi, who had disappeared from his home in Indirapuram in Ghaziabad, was picked up from Tilak Nagar area of West Delhi and taken to 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 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.