Coast guard and border guard officials said the boat was overloaded with about 100 people when it sank in the mouth of the Naf river that divides Myanmar from its South Asian neighbour Bangladesh.
"It capsized near Galachar (coastal village in Bangladesh) with nearly 100 people. We recovered two dead bodies. Two people were rescued alive," area Coast Guard commander Alauddin Nayan told AFP.
Nayan said some 40 people in the boat were adult Rohingya Muslims fleeing their villages in Rakhine for Bangladesh.
Nearly 520,000 Rohingya Muslims have fled to Bangladesh in the last six weeks after the military in Buddhist-majority Myanmar launched a crackdown after attacks by Rohingya militants.
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