Ishrat, 19, was shot dead along with three others near Ahmedabad. Gujarat police officers alleged that they were plotting to kill then Chief Minister Narendra Modi.
Allegations that the Congress-led UPA may have tried to manipulate terrorist David Coleman Headley's testimony on Ishrat Jehan's alleged terror links resurfaced today with sharp focus on an investigating officer who was not allowed to appear before the CBI.
NDTV has learnt that the National Investigation Agency (NIA) officer who interrogated David Headley in 2010, Loknath Behera, had been sought out by the CBI. But he was stopped from testifying by then Home Minister Sushil Kumar Shinde.
Mr Shinde's predecessor P Chidambaram is already facing allegations that he changed the government's document submitted in court to say that there was no proof that Ishrat, shot dead by the Gujarat Police in 2004, was a terrorist.
Ishrat, 19, was shot dead along with three others near Ahmedabad. Gujarat police officers alleged that they were plotting to kill then Chief Minister Narendra Modi.
Mr Behera, who was the part of a NIA team that travelled to the US to question Healey, had noted in case files how the terrorist recalled a conversation between one Muzammil who was in charge of the terror group Lashkar e Taiba's India operations and the group's commander Zaki Ur Rehman Lakhvi.
Headley told investigators that he had heard Lakhvi saying that the Ishrat Jehan operation had failed, which was seen to connect her killing to a Lashkar plot.
But this remained in the case files and did not make it to the NIA charge-sheet, which is being held up by the BJP as another example of the UPA's attempt to manipulate the case.
Sources close to Mr Behera say that while the CBI wanted to incorporate his findings into their probe, it was scuttled by Mr Shinde.
Mr Shinde, when contacted by NDTV, said none of this happened in his tenure, even though he was home minister in 2012-2014 and the CBI's charge-sheet in June 2013 had no mention of Ishrat's antecedents.
The Special Investigation team or SIT, which inquired into the Ishrat case before the CBI, also tried to access the Headley deposition. In a 2011 letter that has now emerged, the team's Karnail Singh asked for permission but the NIA called it 'hearsay'.
Commenting on this, the man who headed the Special Investigation Team for a few months, BJP MP Satyapal Singh, told NDTV that the UPA "had two agendas, to show Ishrat as innocent and to prove it was a fake encounter."