In an urgent directive issued on Sunday, the ministry instructed relevant agencies to investigate the cause of the accident, strengthen safety oversight and prevent similar incidents.
The speedboat, carrying 32 Indian tourists and three crew members, capsized at about 1 pm near May Rut Islet while travelling to An Thoi Port. Authorities said 15 people had been confirmed dead by 3 pm.
The ministry extended its condolences to the victims' families and wished those injured a swift recovery.
The ministry ordered maritime, inland waterway and registration authorities to investigate the accident, assist victims and review safety procedures in coordination with border guards, the coast guard, police and local authorities.
Authorities were instructed to inspect passenger water transport operations nationwide, particularly services linking the mainland with islands such as Phu Quoc, Ly Son, Con Dao, Cat Ba and Halong Bay.
The directive also called for stricter checks on vessel safety, lifesaving equipment, crew qualifications, passenger boarding procedures, vessel registration and technical inspections, particularly during adverse weather.
The directive also called for stricter inspections at ports and passenger terminals, as well as stricter enforcement of waterway safety regulations.