Local administrator Joynul Bari said on Thursday that France's Doctors without Borders (MSF), Action Against Hunger (ACF) and Britain's Muslim Aid UK have been told to suspend their services in the Cox's Bazaar district bordering Myanmar.
"The charities have been providing aid to tens of thousands of undocumented Rohingya refugees illegally. We asked them to stop all their projects in Cox's Bazaar following directive from the NGO Affairs Bureau," Bari told the AFP news agency.
Bari said the charities "were encouraging an influx of Rohingya refugees" from across the border in Myanmar's Rakhine state in the wake of recent sectarian violence that left at least 80 people killed.
The charities have provided healthcare, training, emergency food and drinking water to the refugees living in Cox's Bazaar since the early 1990s.
MSF runs a clinic near one of the Rohingya camp which provides services to 100,000 people.
Speaking a Bengali dialect similar to one in southeast Bangladesh, the Rohingyas are Muslims seen as illegal immigrants by the Buddhist-majority Myanmar government and many Burmese.
They are viewed by the United Nations as one of the world's most persecuted minorities.
Obaidur Rahman, country head of Muslim Aid UK in Bangladesh, confirmed to AFP that his group had stopped its Rohingya project following the order.
The government says some 300,000 Rohingya Muslims are living in the country, the vast majority in Cox's Bazaar, after fleeing persecution in Myanmar. About 30,000 are registered refugees who live in two camps run by the United Nations.
In recent weeks, Bangladesh has turned away boats carrying hundreds of Rohingya fleeing the violence in Myanmar despite pressure from the United States and rights groups to grant them refuge.
Myanmar security forces opened fire on Rohingya Muslims, committed rape and stood by as rival mobs attacked each other during the recent wave of sectarian violence, New York-based Human Rights Watch said Wednesday.
The authorities failed to protect both Muslims and Buddhists and then "unleashed a campaign of violence and mass roundups against the Rohingya", the group said in a report