Occupants of the vessel are said to have set it on fire moments before their arrest
The Mozambican authorities are detaining 12 Iranians caught allegedly shipping drugs off the coast of the northern province of Cabo Delgado.
The boat was intercepted on Saturday in a joint operation carried out by the Mozambican navy and the National Criminal Investigation Service (Sernic).
The interception occurred about 50km (31 miles) from the Mozambican coast.
Police say the fire destroyed approximately 1.5 tonnes of heroin suspected to be on board.
They then jumped off the ship into the Mozambique Channel. Three of them died, while 12 others were rescued by the navy.
The suspects, all of the Iranian nationality, are being detained in the provincial capital, Pemba.
Local media reports indicate the operation resulted from intelligence gathered from the various agencies involved in fighting against drug trafficking.
