The bodies of 15 women and 11 children were recovered in Cox's Bazar after the vessels, which carried an unknown number of Rohingya, sank in the Naf River on Wednesday, Bangladesh border guard commander Lieutenant Colonel SM Ariful Islam said on Thursday.
He added that it was unclear whether anyone was still missing, according to The Associated Press news agency.
The top official in Cox's Bazar, Mohammad Ali Hossain, said the bodies would be buried because no one had claimed them.
Officials in Bangladesh say growing numbers of Rohingya Muslims are trying to cross the Naf river that divides the two countries in rickety boats ill-equipped for the rough waters as they become increasingly desperate to escape the worst outbreak of violence in the restive Rakhine state in years.
One survivor told AFP news agency that the small, overcrowded boat he was travelling on had been tipped over by huge waves where the Naf river opens out into the sea.
"Nobody knew how to navigate the sea waters. When huge waves tilted the boat, we panicked," Shah Karim said.
Residents and activists have accused soldiers of shooting indiscriminately at unarmed Rohingya men, women and children and carrying out arson attacks.
However, authorities in Myanmar say close to 100 people have been killed since Friday when armed men, reportedly from the Arakan Rohingya Salvation Army (ARSA), launched a pre-dawn raid on police outposts in the restive region.
Myanmar authorities say Rohingya "extremist terrorists" have been setting the fires during fighting with government troops, while Rohingya have blamed soldiers who have been accused of carrying out extrajudicial killings.
Thousands flee into Bangladesh
Around 27,400 Rohingya Muslims have crossed into Bangladesh from Myanmar since Friday, three UN sources said, according to Reuters news agency.
The violence comes amid reports of Buddhist vigilantes burning Rohingya villages in Myanmar, Reuters said.
Hundreds of people have been stranded in a no man's land at the countries' border, the International Organization for Migration said.
Satellite imagery analysed by US-based Human Rights Watch indicated that many homes in northern Rakhine state were set ablaze.
Most of Myanmar's estimated one million Rohingya Muslims live in northern Rakhine state.
They face severe persecution in the Buddhist-majority country, which refuses to recognise them as a legitimate native ethnic minority, leaving them without citizenship and basic rights.
Long-standing tension between the Rohingya Muslims and ethnic Rakhine Buddhists erupted in bloody rioting in 2012. That set off a surge of anti-Muslim feeling throughout the country.
Source: Al Jazeera and news agencies