The ship carrying the Bangladeshis will bring back Myanmar security personnel who crossed the border recently amid fighting with rebels
Police were investigating whether it was an act of sabotage and who were behind the incident.
Bakalia Police Station OC Pranab Kumar Chowdhury said no casualties were reported in the incident at a roundabout near Shah Amanat Bridge on Saturday night.
He said the Unique Paribahan bus 'caught fire' when it was being repaired.
The fire crews doused the blazes after they were informed, he added.
Chhatra Dal called the half-day shutdown in Chittagong after Nuru's body was found with his hands and mouth tied on the bank of the river Karnaphuli at Raujan on Mar 30.