"As a first reaction I'm deeply concerned about any arrangement that would involve the blanket return of anyone from one country to another without spelling out the refugee protection safeguards under international law," UNHCR chief Filippo Grandi told the European Parliament.
Lawmakers at the parliament in Strasbourg, France, applauded after he made the comment.
At a summit in Brussels Monday, European Union leaders in principle backed a proposal by Turkey to take back all illegal migrants landing on the overstretched Greek islands.
Turkey also suggested a one-for-one deal under which the EU would resettle one Syrian refugee from camps in Turkey in exchange for every Syrian that Turkey takes from Greece, in a bid to reduce the incentive for people to board boats for Europe.
Turkey is the main launching point for the more than one million migrants who have made the dangerous crossing to Europe since the start of 2015. It is home to 2.7 million refugees from the war in Syria, more than any other country.
But Grandi said the plan did not offer sufficient guarantees under international law, AFP reported.
He said refugees should only be returned to a country if it could be proved that their asylum application would be properly processed and that they would "enjoy asylum in accordance with accepted international standards and have full access to education, work, health care and if necessary social assistance."
He also called for refugees to be screened before being sent away from Greece "to identify highly at-risk categories that may not be appropriate for return even if the above conditions are met."