Following a controversial EU-Turkey deal, the agency has suspended activities at Greek holding facilities. More than 1,600 migrants have arrived in Greece despite the implementation of the agreement.
The UN refugee agency (UNHCR) on Tuesday said it would no longer provide support to mandatory "detention centers" for refugees in Greece.
"UNHCR has until now supported authorities in 'hotspots' on Greek islands, where refugees and migrants were received, assisted and registered," the UNHCR said in a statement.
"In line with the policy on mandatory detention, UNHCR has suspended some activities at all closed centers that are now detention facilities," the organization added.
The agency's decision is a response to the controversial deal struck between the EU and Ankara in March that will effectively allow the bloc to return migrants who reached Greece via Turkey.
In return for Syrian refugees shipped back to Turkey by the EU, the bloc must take in one from a refugee camp in the Anatolian country.
A prior plan to redistribute more than 100,000 asylum seekers from frontline countries, such as Greece and Italy, to other member states proved inconsequential after several Eastern European countries rejected the terms of resettlement.
Meanwhile, the EU-Turkey deal was criticized by human rights groups, with Amnesty International saying the agreement marked "a dark day for Europe and a dark day for humanity."
UNHCR noted that it will maintain a presence "to carry out protection monitoring to ensure that refugees and human rights standards are upheld."
In 2015, more than 800,000 migrants and refugees, many fleeing conflict in the Middle East, Asia and Africa, entered the EU through the Aegean Sea.