Khan, who filed an affidavit in response to the apex court order,said he was removed from the post of field co-coordinator in the Setalvad headed NGO Citizen For Justice and Peace in January 2008, as he refused to "do certain acts which were not in the interest of communal harmony".
Setalvad's estranged aide was responding to the September 2 notice issued by the apex court which had stayed the Gujarat high court's order giving green signal for an investigation against him for allegedly fabricating evidence in 2002 Naroda Gam riot case in which 11 people were killed.
Setalvad and her NGO, which has been working in the state in the aftermath of 2002 riots, has challenged the high court order contending that "it is apparent on the face of the entire proceedings that the attempt has been made to discredit and dissuade them from assisting the victims of the communal riots from getting justice".
Setalvad had opposed the high court order as the probe against Khan could prove troublesome for her as she heads CJP and her former aide had claimed that he was facilitating witnesses in preparing affidavits at the her behest.
The high court had on July 11 rejected the petition filed by the registrar, city civil and sessions court, against last year's magisterial court order for lodging of FIR against Khan and initiating an inquiry under Section 156(3) of CrPC.
The court has also permitted the police to go ahead with the probe on the basis of the FIR lodged against Khan.
The FIR was lodged after a special court, hearing the Naroda Gam riots case, ordered that a criminal complaint be registered against Khan for "fabricating" evidence in December 2010.
It had asked the sessions court's registrar to lodge a complaint against Khan and his associates and dismissed his plea to treat him as a witness in Naroda Gam case.
Khan, who had worked closely with Setalvad, made several allegations against her including that she had warned him of "dire consequences" if he will go against her.
"During the last two-and-half years I was leading a very quiet life with my family in Ahmedabad without mingling in the society. I was continuously getting threatening calls from Setalvad's men during this period for not speaking anything against her.
"I was warned of dire consequences, if, go against her. I was even asked to leave Ahmedabad and settle elsewhere by these callers. I lodged police complaints also about such threats in Rakhial Police Station, Ahmedabad but no action was taken by the police till date," he said in the affidavit.
Khan, who confessed that he was facilitating witnesses in preparing affidavits at her behest, said Setalvad "use to send instructions and fully prepared affidavits" in his e-mail accounts, the passwords of which was also known to her.
He said most of the victims and witnesses were poor and uneducated but still their affidavits were prepared in English on the pretext that Gujarati was not accepted in the high court and the apex court with the help of a particular advocate and court notary.
The affidavit said Setalvad was working with vengeance and she used to instruct him to collect evidence from "wherever" or "create" to fix the accused persons.
The former aide of Setalvad said in the affidavit that relief camps started by the NGOs and the Gujarat government for riots victims had "started becoming hub of political activities" where he along with her used to visit regularly.
Khan, who was also not conversant with English, said though he was working in the NGO, he was provided with an identity card of an English magazine with which Setalvad was associated.
He opposed the petition filed by her and the NGO in the apex court saying it was aimed at "hampering" the investigation done by the authorities to unravel the entire truth.