Mansukh Hiran was subsequently killed as Waze thought him to be the 'weak link' in the conspiracy, the NIA stated.
Besides Waze, former 'encounter specialist' Pradeep Sharma and a few other former police personnel are also accused in the case.
A 1990-batch officer of the Maharashtra cadre, Waze, also known as an "encounter cop", was earlier suspended after his arrest by the National Investigation Agency in the SUV-cum-murder case on March 13.
The recovered some "incriminating" documents and electronic evidence such as laptop, I-pad and mobile phones from Waze's office there, the official said.
Under flak for the 'mishandling' of the bomb scare outside Mukesh Ambani's residence, the Maharashtra government on Wednesday transferred Mumbai Police Commissioner Param Bir Singh from the post.
The NIA also conducted a raid at the residence of Shiv Sena leader and former 'encounter specialist' of Mumbai Police, Pradeep Sharma in connection with the Antilia bomb scare and Mansukh Hiren murder case on Thursday, sources said.