The derailment early on Monday forced railway authorities to cancel five train services from the port city.
But railway officials said that trains will resume in the afternoon.
The engine and two carriages of the Mymensingh Express went off the track around 3:30am at Baratakia of Mirsarari, while the train was on its way to Chittagong from Mymensingh.
"The train’s engine and carriages have spilled over to another track. No train can now pass as it's blocking both the tracks,” said Chittagong Railway Station Manager Abul Kalam Azad.
Five including the train’s driver have suffered minor injuries, he said.
Buses, trains and other transports have been targeted by pro-blockade elements since BNP chairperson Khaleda Zia announced an indefinite nationwide transport blockade from Jan 5.
Railway Eastern Zone's Transport Officer Firoz Iftekhar told bdnews24.com 120 Pandrol clips—used to fasten tracks with sleepers — of around 126 feet railway line have been removed.
Two salvage trains from Chittagong and Sylhet's Laksham have reached the spot and started rescue operations, said Eastern Zone Railway General Manager Mozammel Haque.
He said they hope rail links will resume in the afternoon.
A four-member committee headed by Firoz Iftekhar have been formed to probe the incident.
Trains that left Dhaka and Sylhet at night could not reach Chittagong due to the derailment while Dhaka-bound Turna Express, which left the port city Sunday night is stuck at Sitakunda.
Chittagong Railway Station authorities cancelled services of Dhaka-bound trains—Mahanagar Prabhati, Subarna Express, Mahanagar Godhuli, Karnaphuli Express— and Chandpur bound Sagarika Express.
Hundreds of passengers and concerned relatives were seen waiting at the Chittagong train station after the news broke.
They remained stuck until 11am, after which the authorities announced the cancellations.
Subarna was scheduled to leave station at 6:40am, Prabhati at 7am, Karnaphuli at 10am, Godhuli at 3pm and Sagarika at 7:40am.