The probe body, headed by Joint Secretary Shahnewaz Dilruba Khan, was asked to submit the investigation report within seven working days, said an official release.
It said necessary steps will be taken once the report is submitted.
The release said a report published in different dailies on Monday and aired by a television channel on the death of the teenage patient drew attention of the ministry.
Claiming that the report not fully correct, it said there is no additional or assistant secretary or any official named Abdus Sabur Mondol in the Shipping Ministry and no official car of the ministry or any agency under it crossed the Padma River using Kathalbari-Shimulia ferry route on that day.
According to a report published in different national dailies, a sixth grader who was in an ambulance on a ferry died on Sunday as the authorities allegedly delayed the departure of a ferry at Kathalbari jetty in Madaripur for Abdus Sabur Mondol, an additional secretary to the Shipping Ministry.