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European countries have "fundamentally failed" to fulfil their promises to relocate refugees and asylum-seekers leaving thousands of people abandoned in Greece and Italy, Amnesty International says.

The relocation scheme was agreed in September 2015 and offered around 120,000 refugees and asylum-seekers fleeing war and persecution the chance to rebuild their lives.

So far, European countries have fulfilled less than a third of their asylum relocation commitments.

The worst offenders are Poland and Hungary, both of which have refused to accept a single refugee from Italy and Greece.

Slovakia has only accepted 16 of the 902 asylum-seekers it was assigned, after unsuccessfully challenging the relocation scheme in the European Court, while the Czech Republic has only accepted 12 of 2,691.

Malta is the only EU country to have fulfilled its quota, while Norway and Lichtenstein opted into the scheme voluntarily and have both met their target of 1,500 and 10 respectively.

Belgium has fulfilled 25.6 percent of its quota, the Netherlands has fulfilled 39.6 percent of the target it committed to, and Portugal 49.1 percent.

"Two years after this scheme was agreed, most EU member states have fundamentally failed refugees and asylum-seekers, shirking their responsibilities and leaving thousands abandoned in Italy and Greece," Iverna McGowan, Director of the Amnesty International European Institutions Office, said.

The deadline for relocation ends this September, but Amnesty says governments must continue to relocate eligible refugees in line with their obligations.

"This isn't about paying lip service to doing right by refugees and asylum-seekers, it is a legal obligation", McGowan said.

"EU countries must now step up and make good on the promises they made, or risk being taken to the European Court and potentially facing tough penalties."

Thousands of people, many of them Syrians fleeing war, are stuck in Greece's Aegean islands as a result of an EU-Turkish agreement that curbed the influx of migrants to the European Union.

Asylum-seekers trapped in overcrowded refugee camps have tried to kill themselves amid desperate conditions and an escalating mental health crisis.

More than 100,000 refugees have made the treacherous journey across the Mediterranean Sea to reach Europe in 2017, with 2,247 dying in the process.