Sanjiv Bhatt had filed an affidavit in the Supreme Court in which he said he was present during the meeting in which Modi had allegedly instructed police to give the rioters room to "vent out their anger" and to "teach a lesson" to those involved in Godhra train burning incident.
SIT lawyer R S Jamuar told the metropolitan magistrate B J Ganatra's court that the investigating agency has independently inquired into what had transpired in the meeting.
The court is hearing a protest petition by Zakia Jafri, wife of Congress leader Ehsan Jafri killed in the riots, seeking filing of charge sheet against Narendra Modi and 58 others who she had named in her complaint filed before the Supreme Court.
She had also sought further investigations by an independent agency other than the SIT.
In the 2002 riots, around 1,000 people, majority of them Muslims, were killed.
Zakia in her petition has included the statements made by Bhatt on the alleged instruction given by Modi in that meeting.
"Sanjiv Bhatt says that he attended the meeting. But if he had attended, then he should have informed his senior officer G C Raigar about the developments of the meeting.
Raigar has said that Bhatt never told him about any meeting that the latter attended," Jamuar argued.
"Also, Bhatt sent a wireless message to IPS officer Rahul Sharma asking him to confirm whether slain minister Haren Pandya was present at the high-level meeting convened by the Chief Minister. If Bhatt was present in the meeting, which is what Zakia Jafri has stated in the protest petition as evidence, then why should he ask Rahul Sharma whether Pandya was present in the meeting or not that night," Jamuar argued.
When Sharma said Pandya was not present in the meeting on the night of February 27, Bhatt again asked Sharma to verify and confirm whether he was there or not, Jamuar added.
Bhatt did not attend Modi's Feb 2002 meeting, says SIT
Arguments from SIT's side, which has given a clean chit to Modi and others, are going on a day-to-day basis in the court. Zakia's lawyer will present her case after SIT completes its arguments.
To Bhatt's comments that Modi had asked police forces to go soft on rioters, Jamuar said the Chief Minister never made such a statement and instead he asked the police forces to take all possible steps to control the situation.
"Are all the officers - bureaucrats, DGP, Ahmedabad Police Commissioner telling lies? Is only Sanjeev Bhatt speaking truth? Everybody present in that meeting denied the presence of Bhatt and also denied any such statement made by Modi," Jamuar said.
"The meeting was attended by Gujarat Chief Minister Narendra Modi, bureaucrats, then Director General of Police K Chakravarti and Ahmedabad Police Commissioner P C Pandey," Jamuar told the court in Ahmedabad.
In the meeting, Modi had said the Godhra incident was a "pre-planned, cold-blooded act of terror but the state government was in favour of maintaining communal harmony," Jamuar said.
"In the meeting, Modi said there will be no complacency in investigating the incident. Stern action should be taken against the culprits," Jamuar told the court.
"What then is expected of a Chief Minister? Modi said culprits will be caught and punished. Even US President Barack Obama had said after the Boston terror attack that culprits will be caught and punished."
He said that on the day when the train burning incident took place, Modi was in the assembly as the state government's budget was being presented.
When information about the incident arrived, Modi inquired with the central government, Jamuar stated, adding that after presentation of the state budget, he left for Vadodara at 4 pm, from where he took a private helicopter for Godhra and inspected the incident site before returning to Ahmedabad and convening a high-level meeting.
Regarding bringing back bodies of persons who died in the train burning incident, Jamuar said, "should the Chief Minister have invited persons from across Gujarat to Godhra, which was curfew-bound, to collect bodies of their kin?"
As a majority of the bodies were of the persons who were from Ahmedabad and nearby areas, they were brought to Sola Civil Hospital on the outskirts of the city, Jamuar said, adding the decision was unanimous taken in consultation with Godhra District Magistrate Jayanthi Ravi.
The bodies were brought in a matador escorted by police personnel, who were replaced thrice during the journey, within three and a half hours, covering a distance of close to 130 km, Jamuar added.