The home ministry also ordered a probe by the Computer Emergency Response Team-India to ascertain whether there was hacking of government software systems as there have been several instances where licences of NGOs under scrutiny were renewed automatically.
The home ministry said exercising the powers conferred under Foreign Contribution (Regulation) Act, the registration of Sabrang Trust has been suspended for a period of 180 days with effect from September 10, 2015.
Gujarat police opposed in the Supreme Court the anticipatory bail plea of Teesta Setalvad.
The order said the NGO has transferred an amount of Rs 2.46 lakh from its foreign contribution designated account to Sabrang Trust domestic account, thus mixing of domestic and foreign funds and violating the rules.
Two non-government organisations run by social activist Teesta Setalvad and her husband have been served notice by the home ministry for alleged violations of the Foreign Contribution Regulation Act and asked to reply within 15 days.
The Supreme Court on Wednesday questioned the CBI and the Gujarat government as to why they want to send social activist Teesta Setalvad and her husband Javed Anand back in jail after they have been out for over seven years on anticipatory bail.
Religious tolerance in India is "deteriorating" while religious freedom violations are "increasing", a rights expert has told American lawmakers.
The Apex court, however, said that the interim order providing protection from arrest to Setalvad and her husband Javed Anand shall be extended till the larger bench takes up the matter.
The Gujarat government, which sought a probe into the role of activist Teesta Setalvad's NGO, is now targeting her main funding source, the US-based NGO, Ford Foundation.
The CBI on Wednesday registered a case against social activist Teesta Setalvad and her organisation for alleged violation of FCRA in recieving funds from abroad without taking prior permission from the home ministry.
'Little about this regime, given its vindictive credo, is a complete surprise. But we were still taken aback by the CBI raid as it was a complete abuse of due process.' 'These are not legal inquiries, but abusive use of State power. They are not legitimate investigations, but a witch-hunt.' 'Ours is a typical, classic case of the State and its organs being used as an outlet for motivated vendetta of the vilest kind.'
An FIR has been lodged against social activist Teesta Setalvad, her husband Javed Anand, Zakia Jafri's son Tanvir Jafri and two others for allegedly usurping Rs 1.51 crore collected by them for turning Gulbarg Society into a museum, police said.
The activist and her husband have allegedly embezzled funds from riot victims.
"Whose money is this? From where did the money in these bank accounts have come," a bench headed by Justice Dipak Misra asked the counsel for Setalvad.
The two were arrested for alleged embezzlement of funds for a museum in Ahmedabad.
The court while granting bail to the duo also held that it does not find any possibility of the accused persons fleeing from justice and that their custodial interrogation was not required.