The Balkan trail from Greece to northern Europe used by refugees has been blocked after a string of nations slammed shut their borders.

Slovenia and Croatia, two of the countries along the well-trodden route, said late on Tuesday that no refugees wishing to transit towards other countries would be allowed to enter.

Serbia indicated it would follow suit.

EU member Slovenia said that from midnight (23:00 GMT), the only exceptions were for people wishing to claim asylum in the country or for refugees "on humanitarian grounds and in accordance with the rules of the Schengen zone".

READ MORE: UN says EU-Turkey refugee deal would violate law

The measures follow Austria's decision in February to cap the number of refugees passing through its territory, and Foreign Minister Sebastian Kurz late on Tuesday welcomed the news.

In Greece, however, the tightening of border restrictions in recent weeks sparked by Austria's move has created a bottleneck at the border with Macedonia where more than 13,000 people were stranded, according to state agency ANA.

There was no official reaction from Athens to Slovenia and Croatia's moves but a Greek government source told AFP news agency on Wednesday that it now considered borders through the Balkans as "de facto closed".

The authorities were trying "to convince the refugees that are stuck to go temporarily to welcome centres throughout Greece," the source said.

Merkel's open door

More than a million people have crossed the Aegean Sea into Greece since the start of 2015, many from Syria, Afghanistan and Iraq and most aiming to reach wealthy Germany, Austria and Scandinavia.

This has caused deep divisions among EU members about how to deal with Europe's worst refugee crisis since World War II, and put German Chancellor Angela Merkel under severe pressure domestically over her open-door asylum policy.

Merkel hopes that a mooted deal with Turkey discussed at an EU summit on Monday, and due to be finalised on March 17-18, will be the answer, with Turkey offering to take back all "illegal migrants" landing on the Greek islands.

Turkey, currently hosting 2.7 million refugees escaping the five-year-old civil war in neighbouring Syria, is the main springboard for making the perilous sea crossing to Greece.

Ankara proposed an arrangement 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.

In return though, Turkey wants six billion euros ($6.6bn) in aid, visa-free access for Turkish citizens to Europe's passport-free Schengen zone and a speeding up of Ankara's efforts to join the EU.

European Commission chief Jean-Claude Juncker called the plan a "real game-changer" and insisted it was "legally feasible", but it has sparked concern from UN refugee chief Filippo Grandi and others.

Rights group Amnesty International said the proposal was full of "moral and legal flaws" and along with Human Rights Watch challenged the idea that Turkey was a "safe country" to which refugees could return.