"I would not know because it was not done at my level. I would say it was done at the political level," he told Times Now channel when asked whether the affidavit was changed at the political level.
The then UPA government had submitted two affidavits - one that the four, who were killed in an alleged fake encounter, were terrorists and the second saying there was no conclusive evidence - within two months in 2009.
Pillai said Jahan could be an unwitting player in the hands of Pakistan-based terror group LeT and favoured a probe into the statement of David Headley on her terror links.
The former home secretary said that there was no doubt that those killed in the alleged fake encounter in Gujarat had links with Lashkar.
"They were LeT activists. She (Ishrat) knew that something was wrong. Otherwise an unmarried young Muslim woman would not have gone with some other men," he told reporters.
Commenting on whether it was a fake encounter, Pillai said the CBI had already investigated that issue and filed a charge sheet.
"The real issue is whether it was a real encounter or fake. The CBI had probed that," he said.
The former bureaucrat said LeT did put her name on their website as a martyr, which was later withdrawn. "There was no direct evidence, except that LeT put her name on the website. So, I would say may be she was an unwitting player."
Complimenting the intelligence bureau, Pillai said it was a highly successful operation and the IB knew well before that the LeT people were coming.
Asked about Headley's statement before a Mumbai court that the 19-year-old Mumbra girl was a LeT member, he said it was a matter of investigation. "I think there should be further investigation into Headley's statement."
The CBI, which took over the probe from the Gujarat high court appointed special investigation team, had filed a charge sheet in August 2013 saying the encounter was fake and executed in joint operation by the city crime branch and subsidiary intelligence bureau.
The CBI had named in its charge sheet former Special Director in Intelligence Bureau Rajinder Kumar and three other IB officials with murder and criminal conspiracy in the Ishrat encounter case. However, the home ministry had denied sanction to prosecute the IB officials.
Ishrat, Javed Shaikh, Amjadali Akbarali Rana and Zeeshan Johar were killed in an encounter with the Gujarat police on the outskirts of Ahmedabad on June 15, 2004. The city crime branch had then said that they were LeT terrorists and had landed in Gujarat to kill the then Chief Minister Narendra Modi.
Headley deposition ends; says Lashkar knew Pak would take only 'superficial' action post 26/11
'Headley's testimony on Ishrat Jahan is like KBC'
Headley said what we have been saying all along; Ishrat encounter was genuine: Vanzara
Can you call Ishrat's a fake encounter?
Don't care what Headley is saying; she was innocent: Ishrat's sister