"We've ordered people in low-lying river shoal areas to evacuate to cyclone shelters," Chittagong government administrator Mohammad Abdullah said, saying several hundred thousand people were covered by the order.
Earlier on Wednesday the UN said the cyclone appeared to have weakened, but still posed a risk to more than eight million people.
Cyclone Mahasen may still bring "life-threatening conditions" for 8.2 million people in northeast India, Bangladesh and Myanmar, it warned, adding Bangladesh's Chittagong and Cox's Bazaar areas could face the worst of a tidal surge and heavy rains.
Cox's Bazaar, a long strip of coastline, is home to ramshackle camps housing many of the estimated 300 000 Rohingya Muslim refugees living in Bangladesh.
Local officials said 113 medical teams had been mobilised to deal with the impact of the cyclone and leave had been cancelled for all government employees.
Ready
"We've made all the preparations to face the cyclone," Mohammed Kamruzzaman, a government magistrate in charge of a Rohingya refugee camp in Cox's Bazaar, told AFP.
"We have been using loudspeakers to alert both documented and undocumented Rohingya refugees of the dangers of the cyclone.
"We've also stockpiled dry food, kept medical teams and ambulances on stand-by and shifted the sick and pregnant women from the camps to hospitals."
Bangladesh's disaster management minister Mahmud Ali told reporters that the government had made "all-out preparations for the cyclone in all 13 coastal districts".
Experts say Bangladesh is better prepared to handle cyclones than authorities across the border in Rakhine, where tens of thousands of Rohingya made homeless by communal unrest last year languish in flood-prone camps.
Myanmar state media late on Tuesday said rescuers were searching for 58 missing Rohingya whose boat capsized after hitting rocks in a coastal waterway after they fled the cyclone's path to escape to higher ground.
Too late
A number of other Rohingya in Myanmar have expressed reluctance to relocate, reflecting deep mistrust of security forces following two outbreaks of violence last year that left about 200 people dead and whole neighbourhoods razed.
Rights groups have accused Myanmar security forces of complicity in the unrest.
OCHA said Myanmar planned to move at least 38 000 internally displaced persons out of the cyclone's track by Tuesday, but added that it was unclear how many had actually been relocated.
Myanmar's army has been mobilised to help evacuate those most at risk. But some rights campaigners said the effort had come too late after months of warnings of the danger posed to the camps by this year's monsoon.