The suspect was hiding in a house in Kakori area. The densely populated neighbourhood was cordoned off and at least 20 commandos were involved in the operation, police said.
The blast occurred in a general coach of the train between 9.30am and 10am when it was on its way to Ujjain from Bhopal, Railway PRO, Indore, Jitendra Kumar Jayant said.
He recalled that democracy-lovers had fought a big battle against the Emergency.