At least 12 people died and scores were missing on Monday after a boat packed with Rohingya refugees — many of them children — capsized, the latest tragedy to strike those fleeing violence in Myanmar's Rakhine state.

Coast guard and border guard officials said the boat was overloaded with about 100 people when it sank late Sunday in the mouth of the Naf river that separates Myanmar from Bangladesh.

Border Guard Bangladesh (BGB) official Abdul Jalil told AFP 12 bodies had been recovered after an all-night rescue operation, saying "they include 10 children, an elderly woman and a man".

Area coast guard commander Alauddin Nayan said the boat capsized near the coastal village of Galachar with nearly 100 people on board.

He said some 40 people in the boat were adult Rohingya Muslims fleeing their villages in Rakhine.

"The rest were children," he said.

Border guard boats have rescued 13 Rohingya including three women and two children after scouring the estuary of the Naf river, Jalil said.

Since the boat capsized near the Myanmar side of the border, Jalil said many may have swum to the Rakhine coast.