Thousands of Rohingya men and women lined up in intense heat at makeshift health centers, many with young children in their arms, to receive the oral vaccine against the disease.
The UN is working with the Bangladesh government to vaccinate 650,000 people living in the sprawling camps against cholera, which spreads through dirty water and can kill if left untreated.
"These people lack most of the basic services -- toilets, water sanitation and everything," UNICEF spokesman A M Sakil Faizullah told AFP.
"When we have this kind of situation, there's a heavy possibility of a cholera outbreak."
Nearly 520,000 Rohingya Muslims had arrived in Bangladesh since late August, fleeing a military crackdown in mainly Buddhist neighboring Myanmar that the UN has said likely amounts to ethnic cleansing.
Poor and overpopulated Bangladesh has struggled to cope with the mass influx of people, many of whom have to travel for days or even weeks to reach safety and arrive exhausted and malnourished.
The influx had slowed in recent weeks, but now appears to have picked up again and an estimated 11,000 new refugees arrived on Monday.
The UN refugee agency said Tuesday it was working with the Bangladesh authorities to set up a transit center in preparation for a fresh influx from Myanmar's Rakhine state.
Many of the new arrivals are from the Buthidaung district of Rakhine which lies relatively far from the border.
They told AFP the army in Myanmar had prevented them from buying food, making it impossible for them to stay.
Dozens more are feared to have drowned when a boat packed with desperate refugees sank late on Sunday night.
Bangladesh police said Tuesday they had found 14 more bodies, taking the number of confirmed dead to 28, with scores more missing.
The treatment of the Muslim minority has sparked international condemnation of Myanmar and its de facto leader Aung San Suu Kyi, a Nobel peace laureate.
On Tuesday her party, the National League for Democracy [NLD], held a peace rally in Yangon attended by around 40,000 people.
NLD lawmaker Win Maung said ahead of the ceremony it would show the world that people of different faiths could live in harmony in Myanmar.
"We deeply regret the reaction from international countries based on the news without truth," said the lawmaker.
World Health Organization [WHO] workers and local volunteers will vaccinate 650,000 Rohingya over the coming weeks and then follow up with a second dose of the vaccine for an estimated 250,000 children aged between one and five.
It the second biggest such campaign ever, after 800,000 people were immunized against the disease in Haiti in November.
The WHO's Bangladesh representative N Paranietharan called it a "huge undertaking" and said he was confident an outbreak would be averted.
He said thousands of Bangladeshis living near the refugee camps would also be vaccinated.
Cholera was a major killer in Bangladesh until in the 1970s, but the country has seen major improvements in sanitation facilities since then.
The Rohingya are a stateless Muslim minority who have long faced persecution in Myanmar, which regards them as illegal immigrants from Bangladesh.
The UN said more than 600,000 have arrived in the last year, swelling camps that were already home to between 300,000 and 400,000 refugees.
Bangladesh has allocated land to accommodate some 800,000 refugees in one massive camp, but the UN has warned that such a large concentration in one area could promote the spread of disease.