Gopinath Pillay, the father of Pranesh Pillai alias Javed Sheikh, one of those killed alongwith Ishrat, has moved the court with the petition.
The special CBI court judge Geeta Gopi issued the notice to Shah and Kaushik as well as the CBI while posting the plea for further hearing on March 26.
Pillay wants the court to put the two on trial for criminal conspiracy, illegal confinement and murder.
Mumbra-based Ishrat Jahan was allegedly murdered with her friend Javed Sheikh alias Pranesh Pillai and two others (believed to be Pakistani nationals) on June 15, 2004 by Gujarat police in a fake encounter outside the city.
Pillay' application states that there was "a clear prima facie case" against Amit Shah on the basis of the material collected by CBI.