Hundreds of thousands of Muslim Rohingya have fled Myanmar in past decades to escape persecution [AFP]

Around 85 people are missing after another boat carrying Rohingya refugees towards Malaysia sank off Bangladesh, the second such tragedy in less than a fortnight, officials have said.

Bangladesh Border Guard commander Lieutenant Colonel Zahid Hasan said the vessel was carrying around 110 passengers when it went down off early on Wednesday around 15km off the southern Cox's Bazaar coastal district.

"We have now rescued 25 survivors with the help of local fishermen and a search and rescue operation is underway," Hasan told AFP.

"The boat was heading to Malaysia illegally," he added.

Hasan confirmed that at least two of those who had been rescued were Rohingya and that they were all being kept in custody.

Lieutenant Badruddoza, a commander in the coast guard who uses only one name, said that a search and rescue operation was being conducted in conjunction with the Bangladesh navy.

The latest tragedy comes after a boat carrying some 135 passengers, mostly Muslim Rohingya refugees who had fled unrest in neighbouring Myanmar, sank in the Bay of Bengal on October 28.

Only around half a dozen made it to safety.

Hundreds of thousands of Muslim Rohingya have fled Myanmar in past decades to escape persecution, often heading to neighbouring Bangladesh, and recent unrest has triggered another exodus.

Since the unrest erupted, Bangladesh has been turning away boatloads of fleeing Rohingya. The policy has been criticised by the United Nations but Bangladesh said it was already burdened with an estimated 300,000 Rohingya.

Myanmar's 800,000 stateless Rohingya, described by the UN as among the world's most persecuted minorities, are seen by the government and many people in Myanmar as illegal immigrants from Bangladesh.