Bangladesh had ordered three international NGOs to stop operating in the border area.
EU Humanitarian Aid Commissioner Kristalina Georgieva said that she was deeply concerned about the situation of the Rohingyas.
“I strongly appeal to the Government of Bangladesh to act responsibly and offer a helping hand to all those in need, and to allow humanitarian aid organizations to do their work for the benefit of all communities,” she said in a statement.
More than 800,000 Rohingya Muslims live in Myanmar, but they are not recognized by the government as one of its ethnic groups.
Deadly summer riots between the Muslim Rohingya and Buddhist majority have forced many to flee to neighboring Bangladesh.
A further 200,000 are living undocumented in Bangladesh, according to the office of the UN High Commissioner for Refugees.
Bangladesh has continued to turn back many refugees, and last week told three NGOs to stop providing food and other humanitarian aid to Rohingyas. It said the assistance could encourage more people to try to cross the border from Myanmar.