The NIA said in the charge sheet the explosion had targeted Pakistani Muslims.
The incident happened at Diwani village near the industrial town of Panipat, 160 kilometres from here, in Haryana, when it was heading towards Attari, the last station on the Indian side.
Aseemanand, a member of the right-wing Hindu group Abhinav Bharat, was alleged to be involved in the bombing.
Lokesh Sharma, Sunil Joshi, Sandeep Dange and Ramchandra Kalasangra alias Ramji were also named in the charge sheet.