The charity says Europe's response to the crisis has been "shameful" and threatens the "very of concept" of the refugee.
Medical aid charity Medecins Sans Frontieres (MSF) has said it will no longer accept funding from the European Union (EU) and its member states because of the bloc's "shameful" and "damaging" migration policies.
Under an agreement struck in March to stem a human tide that brought a million refugees and migrants to the continent in 2015, Turkey agreed to halt illegal migration through its territory in return for financial and political rewards.
MSF, which is also known as Doctors Without Borders, said Europe's focus has shifted to keeping migrants out of the continent rather than helping them.
It also warned the EU-Turkey deal has put in jeopardy the concept of a refugee - someone who is fleeing war and persecution and is entitled to a safe haven.
MSF said 8,000 people - mainly from war-torn Syria, Iraq and Afghanistan - are stranded in Greece as "direct consequences" of the deal and are living in overcrowded camps, sometimes for months on end, in fear of deportation to Turkey and denied legal aid.
Jerome Oberreit, MSF's International Secretary General, said the organisation will lose €37m (£29.1m) of funding from EU states and €19m (£14.9m) from EU institutions as a result of the decision.
In the short term it will cover the shortfall from emergency reserves, he said, adding the charity gets more than 90% of its funding from private donations.
Mr Oberreit said: "For months MSF has spoken out about a shameful European response focused on deterrence rather than providing people with the assistance and protection they need.
"The EU-Turkey deal goes one step further and has placed the very concept of 'refugee' and the protection it offers in danger.
"Is Europe's only offer to refugees that they stay in countries they are desperate to flee? Once again, Europe's main focus is not on how well people will be protected, but on how efficiently they are kept away.
"Europe's attempt to outsource migration control is having a domino effect, with closed borders stretching all the way back to Syria. People increasingly have nowhere to turn.
"Deterrence policies sold to the public as humanitarian solutions have only exacerbated the suffering of people in need. There is nothing remotely humanitarian about these policies. It cannot become the norm and must be challenged."
Under the terms of the agreement, migrants arriving in Greece are meant to be quickly interviewed to determine whether they will be allowed to remain or sent back to Turkey.
The EU takes in one Syrian refugee from camps in Turkey for each irregular migrant returned, in a move aimed at breaking the business model of people smugglers, who have made fortunes by providing spaces in boats to desperate migrants.