Police said on Thursday the 500-page chargesheet was filed on Wednesday in the court of first class railway magistrate P K Joshi by the investigation officer K C Bawa, DSP of Railway Police.
The FIR had alleged that a 1540-strong minority mob attacked the Sabarmati Express on February 27, minutes after the delayed train left the Godhra station on that fateful day.
Fifty-eight people, mostly Ram sewaks returning from Ayodhya, including women and children, were killed in one of the worst ever mob attack on a train.
The incident precipitated large scale violence with hundreds of minority people killed and thousands rendered homeless in Ahmedabad and other parts of north Gujarat.
The chargesheeted names prime accused Haji Bilal, a municipal corporator and Congress supporter. Bilal along with President of Godhra municipality Mohd Hussain Kalota were arrested in March. Others arrested include corporator Abdul Razak and Shiraj Abdul Jamesha.
Bilal, BJP sources alleged, had played a crucial role in installing Mohd Hussain Kalota as the president of the municipality by toppling Raju Darji of the BJP.
The polls to the civic body last year threw a hung house to the 36-member municipal council with the BJP winning nine seats, the Congress five and Independents 22.
Bilal is also alleged to have nexus with gang leader late Latif and was reported to have visited Karachi several times.
Panchmahal SP Raju Bhargav, when contacted, told PTI over phone the chargesheet was filed by Railway Police and the case was being pursued under the supervision of CID crime.