Hasan Mahmud says 150 Bangladeshi citizens stranded in Myanmar will return by ship
Port officials said the channel had been off limits since the accident on Friday morning, 12 nautical miles from Mongla.
No injuries have been reported.
Harbour Master Mohammad Aktaruzzaman said cargo vessel Hajera-1 sank after it rammed into a ship bearing Panama's flag on its way to Khulna.
Eight crew of the vessel swam to the shore.
He said they restricted water traffic as the clinker-laden cargo ship sunk in the main channel.
A Navy team is working to identify the vessel.
Aktaruzzman said the channel would be reopened after the sunken vessel was located.