UN Secretary-General Ban Ki-moon on Friday arrived in Greece for a first-hand look at the migration crisis that has rocked Europe for the past year, including a visit to the flashpoint island of Lesbos.

Ban, who is on a two-day visit, was taken to an Athens solidarity centre providing medical and legal assistance to vulnerable groups and will later meet with Greek President Prokopis Pavlopoulos.

On Saturday, he will fly to Lesbos to meet with some of the thousands of refugees that are stuck in the country, hoping for asylum and facing an uncertain future.

"I continue to stress the need for providing assistance and support to those rescued, ensuring adequate reception condition and access to asylum for those in need of international protection," Ban said in a message to state agency ANA ahead of the visit.

"The rights of men, women and children who were forced to leave, have to be protected at all times, in law and in practice," he said.

The government says over 56,000 migrants -- including over 3,400 on Lesbos -- have been trapped in Greece after Balkan states begun shutting their borders in February to stem a growing influx into wealthy northern Europe.

Most of them are now in state-run camps that aid groups including the UN refugee agency have labelled poorly equipped and inappropriate for a long stay.

Lesbos and other eastern Aegean islands last year were the gateway into Europe for a migration wave unseen since the Second World War.

According to UN figures, Lesbos alone accounted for around 500,000 arrivals in 2015.

A migration deal between the EU and Turkey put into effect in March has drastically reduced the flow, but at the cost of human rights violations according to rights groups.

Since March 20 when the deal came into force, over 460 migrants have been sent back to Turkey, where critics say they face discrimination and possible danger.

And a relocation programme promising to move successful asylum claimants to other EU states has made little headway.

On Friday, medical aid group Doctors Without Borders cited the agreement as one of the reasons behind a decision to stop accepting EU funds.

"MSF announces today that we will no longer take funds from the EU and its member states in protest at their shameful deterrence policies and their intensification of efforts to push people and their suffering back from European shores," the group said in a statement.

Ban's visit to Athens concludes a European tour that also took him to Brussels, Moscow, Saint Petersburg prior to Athens.

It comes as Ban enters the final months of his tenure as UN chief and as the United Nations prepares to host a major international meeting in September on the world refugee crisis.

World leaders are to agree on a new global plan to resettle refugees at the September 19 meeting on the sidelines of the UN General Assembly meeting in New York.