Bhatt had filed an affidavit in the Supreme Court implicating Gujarat Chief Minister Narendra Modi in connection to the riots.
Sources said that the commission has asked Bhatt to appear before it on May 16 after an application filed before it by the Jan Sangarsh Manch, an NGO representing some of the riot victims.
The NGO on Tuesday approached the panel, requesting it to probe the role and conduct of Modi in the wake of the Godhra carnage.
The petition, moved by convener Amrish Patel on behalf of JSM, said that the deposition of Bhatt "will be very important and material evidence" on deciding the role and conduct of the chief minister and others during events that unfolded post-Godhra.
Bhatt, in an affidavit to the Supreme Court, accused Modi of instructing state officials to allow Hindus "to vent out their anger" during the clashes, so that Muslims could be "taught a lesson".
JSM counsel Mukul Sinha had said that it has now become necessary to examine Bhatt in the wake of revelations made by him in the affidavit.
He further said that the state government had itself amended the terms of reference of the Nanavati Commission in June 2002 for enquiring into the role of chief minister and others with regard to post-Godhra riots.
Justice G T Nanavati and Justice Akshay Mehta have already submitted a part of their report dealing with the Godhra train carnage and are in the final stages of submitting their report on post-Godhra riots.
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