Six Bangladeshi vessels fishing near Saint Martin Island, a small outcrop at the mouth of the Naf river that divides the two neighbours, strayed into Myanmar's territorial waters on Wednesday.
Dhaka said Myanmar's navy then attacked the vessels, killing a 60-year-old man and abducting 57 others.
"Bangladesh urges Myanmar to take immediate steps to prevent the recurrence of such unwarranted actions," the foreign ministry said in a statement, adding it had lodged a diplomatic protest.
The other fishermen had since been released after an intervention by the Bangladesh Coast Guard, it said.
Giyas Uddin, an officer from the nearby Teknaf police station, told AFP another fisherman had been wounded by the Myanmar navy's fire.
The Daily Star newspaper quoted one of the vessel's owners as saying that the fishing crews had inadvertently crossed into Myanmar waters due to strong sea currents, adding that the navy had fired without warning.
Myanmar's military junta has not commented on the incident.
Border issues are a perennial source of tension between the two neighbours, with Bangladesh host to around a million stateless Rohingya refugees who fled successive waves of persecution in Myanmar.
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