The apex court instructed the panel's chariman RK Raghavan to take members Shivanand Jha and Geeta Johri off the investigating team till further notice.
The SC order came in response to several petitions filed against Jha, Johri and another SIT member Ashish Bhatia.
Jha and Johri are accused of being involved in the riots.
While, Bhatia is being blamed for trying to sabotage the case by forcing victim-eyewitnesses to change their testimony.
The development came just days after state Chief Minister Narendra Modi appeared before the SIT for questioning in connection with a riots case.