After her detention on Saturday, she had been taken to the Santacruz police station in Mumbai for informing the local police about her detention.
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.
She is accused of having a role in illegal exhumation of bodies of some victims of the 2002 Gujarat riots.
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.
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.
'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.'
The victims of the 2002 post-Godhra violence criticised Gujarat Chief Minister Narendra Modi, on Monday, for not appearing before the Special Investigation Team in Ahmedabad in connection with a riots case and asked him to come clean.
Relatives of victims of the 2002 communal violence in Gujarat Tuesday claimed to have exhumed skeletal remains from a mass grave in Panchamahal district of those believed to have been killed in the post-Godhra riots.
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.
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 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.
'We are losing the battle of secularism, but we have not lost.'
'There is nothing traitorous about highlighting the poor record of your own government. If the Indian government does something wrong, we all have the right to point this out at any forum, international or national.'
The court said that the petitioner can approach a higher court for further investigation in the case.
A bench of Justices A M Khanwilkar and Deepak Gupta said the matter will be heard on November 19, as the court has not gone through the petition in detail.
Journalist-turned-activist Teesta Setalvad in her new book 'Foot Soldier of the Constitution: A Memoir' has spoken of the rise of communalism and the aftermath of the '02 Godhra riots. In this interview with Rediff.com's Syed Firdaus Ashraf, she discusses her book, the cases against her and the state of secularism in the country.