Darko Bandic, File, Associated Press
FILE - In this May 21, 2016 file photo, a boy carries a dish through a flooded part of the migrant camp in Idomeni, Greece. The medical aid organization Doctors Without Borders announced Friday, June 17, 2016 that it will no longer seek European Union funding in protest against the EU's much-maligned migrant deal with Turkey.

BRUSSELS — The Nobel prize-winning medical aid organization Doctors Without Borders announced Friday that it will no longer seek European Union funding, in protest at the EU's much-maligned migrant deal with Turkey.

"The EU deal is the latest in a long line of policies that go against the values and the principles that enable assistance to be provided," Secretary General Jerome Oberreit told reporters in Brussels.

Doctors Without Borders, he said, "will no longer request funds from the EU and its member states."

EU money totaled around 46 million euros ($52 million) in 2015, about 8 percent of the organization's total budget.

Oberreit said Doctors Without Borders, also known by its French acronym MSF, still plans to keep working in Greece and near the Turkey-Syria border but will seek money from other sources to keep its projects going.

The unusual and radical step has been the subject of deep debate within the organization.

Unable to agree among themselves on how best to tackle Europe's biggest refugee emergency since World War II, EU member states have tried to persuade Turkey to stop hundreds of thousands of migrants from coming and to take back thousands more. Almost 3 million refugees are sheltering in Turkey, only around 10 percent of them in government-funded shelters.

The EU-Turkey agreement came into effect on March 20. Under it, all migrants traveling from Turkey to the Greek islands will be sent back unless they qualify for asylum in Greece. For every Syrian migrant who returns, the EU has offered to directly resettle a Syrian refugee already there in a European country.

Europe has offered incentives to convince Turkey to crack down, including up to 6 billion euros in funds for Syrian refugees in Turkey, visa-free travel for Turkish citizens and fast-track EU membership talks.

Non-governmental organizations and even U.N. agencies have expressed concern about the legal and moral implications of the deal.

Oberreit said MSF is refusing to work in partnership with Europe because the EU's effort "is not aimed at providing for those most in need. It is aimed at ... border control."

The EU's executive Commission, which provided MSF with around 15 million euros last year, said that the organization had not asked for European funding for projects in Turkey so no work there would be affected.

Commission spokesman Margaritis Schinas added that "the suspension will have no impact on ongoing EU humanitarian projects implemented by MSF in other parts of the world." MSF noted that it would honor all ongoing projects with EU funding but not seek European institution or government money for future projects around the world.

Belgium, which donates 5 million euros each year to MSF, and Sweden expressed regret over the move.

Belgian Development Minister Alexander De Croo said his country and MSF had always cooperated well on issues like the crisis in Syria or the deadly Ebola outbreak in Africa.

De Croo said he "hopes that in the interests of millions of people in need, constructive collaboration will be possible again."

"It is regrettable. MSF's work makes a big difference," Sweden's Foreign Minister Margot Wallstrom told Sweden's TT news agency. "We share the concern that humanitarian principles are weakened, such as humanitarian organizations do not get access in countries like Syria."

Jan M. Olsen in Copenhagen and Raf Casert in Brussels contributed to this report.