This alleged evidence came as the CBI began to probe the role of the Intelligence Bureau, specifically former Joint Director of the IB in Ahmedabad, Rajinder Kumar, who, it suspects, generated a false intelligence input which led to the encounter.
The CBI's status report on investigations accessed by NDTV says that, the three main alleged conspirators - Rajinder Kumar and DG Vanzara and PP Pandey, both senior IPS officers of the Ahmedabad Crime Branch then - had discussed the Ishrat case two days before the encounter, on June 13, 2004.
The agency has alleged that Rajinder Kumar asked Mr Vanzara and Mr Pandey what should be done with Ishrat and three young men, who were in their custody at that time. The CBI has alleged after speaking to eyewitnesses who were present during these exchanges.
On June 14, Mr Vanzara allegedly told a colleague that he had gotten the go-ahead from "white beard" and "black beard". CBI sources say that this is code amongst Gujarat's cops for Narendra Modi and Amit Shah.
Matching these dates are call records with the CBI, which allegedly show that Mr Vanzara made calls to both senior politicians.
The CBI also allegedly has call data records which establish that Mr Vanzara spoke to Amit Shah at 10:57 pm, five hours before the alleged encounter, which took place in the early hours of June 15, 2004.
Mr Shah and Mr Vanzara also allegedly exchanged calls at 6:07 am and 7:09 am, after the encounter.
These details are expected to be part of the CBI's chargesheet in the Ishrat case to be filed on July 2, next week.
Already, almost 10 police officials have been booked in the case. Mr Vanzara, already in jail for another case, was remanded in judicial custody in the Ishrat case earlier this month.
The BJP has dismissed this as politically motivated, but the CBI claims it has the testimonies of 22 mid-to-lower-ranking policemen who were witnesses to the encounter and its planning.