A bench of justices KS Radhakrishnan and Dipak Misra also asked the state government to quantify the amount needed for building and repairing those sites that were affected by the riots.
The court gave the directions on an appeal filed by the Gujarat government challenging a Gujarat High Court order directing it to pay compensation for damage and destruction of the religious sites.
At the start of the proceedings, the Gujarat government said that the state exchequer could not be used for building and repairing religious sites.
The bench, however, said it would look into the issue whether public funds could be used for restoring the damaged sites.
"You compensate if a house is washed away in a flood or if it is damaged in an earthquake. Then why not in case of a religious place?" the bench asked.
The court directed the state government to file an affidavit with regard to the religious sites affected by the riots and posted the matter for further hearing on Jul 30.
On Feb 8, the Gujarat government was pulled up by the Gujarat High Court for "inaction and negligence" on its part during the 2002 post-Godhra riots that led to large-scale damage and destruction of religious structures.
A high court division bench of Acting Chief Justice Bhaskar Bhattacharya and Justice JB Pardiwala had ordered compensation for over 500 places of worships in the state on a plea by Islamic Relief Committee of Gujarat (IRCG), an NGO.
The NGO had contended that 535 religious places were affected, out of which 37 remain to be repaired.
Challenging the high court's order, advocate Tushar Mehta, appearing for the state government, contended that Sikh religious groups were also seeking compensation for damage to the religious places during the 1984 anti-Sikh riots.
The plea by IRCG in 2003 had sought the court's direction to the government to pay compensation for damage to religious places during the riots on the ground that the National Human Rights Commission, too, had recommended it and the state government had in principle accepted the suggestion.
The high court had observed that inadequacy, inaction and negligence on the part of the state government to prevent the riots had resulted in religious structures being affected across the state.
It had said when the government could pay compensation for destruction of houses and commercial establishments, it should also pay compensation for religious structures.
If the structures have been already restored, the government should reimburse the amount spent on their restoration, the court had said.