European leaders claim to have closed the main refugee route to northern Europe, raising the possibility of tens if not hundreds of thousands of refugees being trapped in Greece while the EU attempts to finalise a deal that could see them all returned to Turkey.

Macedonia, Croatia and Slovenia – three of the countries that lie between Greece and the preferred refugee destinations in northern Europe – all announced on Wednesday that their borders were now shut. Several hundred thousand asylum-seekers have used this route to reach countries such as Germany since it became popular last summer, most of them transported and sheltered by Balkan countries during their journey.

Following the closures, Donald Tusk, president of the European council, claimed that “irregular flows of migrants along western Balkans route have come to an end”. And Slovenia’s prime minister, Miro Cerar, said: “The so-called western Balkan route for irregular migrants is no more.”

In response, analysts and campaigners said that though officials have closed the humanitarian corridor that emerged late last summer, irregular migration would probably still continue throughout eastern Europe, albeit to a lesser extent. Tens of thousands of refugees made their own way through the Balkans in the first half of 2015, despite the opposition of European governments – and this pattern is likely to re-emerge.

The UNHCR, the United Nations’ refugee agency, is preparing contingency plans for when new routes are forged, said Carlotta Sami, a spokeswoman for the organisation.

“We do not think that the closure of the [western Balkan] borders will stem the flow,” said Sami, adding: “If this route closes, we will have new routes with new problems. We are preparing for an increase through Libya, Bulgaria, Turkey to Italy, Libya to Italy – and there is the possibility of more people crossing to Spain.”

On Tuesday, one Syrian who has been trying to leave for Greece from Turkey for a week, told the Guardian that she and others still intended to make the journey. “The trip is illegal anyway, so different rules are not going to deter us,” said Muna, 23, who asked for her full name not to be disclosed. “We as Syrians are used to finding ways round rules now anyway.”

Other expected routes include a maritime one across the Black Sea to Ukraine, and a land route from Greece to Albania – which more than 250,000 people used in the early 1990s after the fall of the Albanian government.

For the past six months, Italian and Albanian officials have met regularly to discuss a coordinated response to the potential reemergence of the Albania-Italy maritime people-smuggling route.

Donald Tusk: travel on the western Balkans route has ‘come to an end’. Photograph: Emmanuel Dunand/AFP/Getty Images

To avoid the situation reaching this point, the EU and Turkey are currently negotiating a deal that could see all arrivals in Greece returned to Turkish soil. Rights groups have said the proposal is unethical, unworkable and illegal, with Amnesty saying it is being “celebrated by people who are dancing on the grave of refugee protection”.

Even if an EU-Turkey agreement were reached, thousands are expected to keep arriving every week on the Greek islands – risking the possibility of a humanitarian disaster, since cash-strapped Greece is unable to properly care for them.

About 1,000 people continue to arrive each day on the island of Lesbos alone, according to the UN refugee agency. Some 35,000 are already trapped in Greece, with that number likely to rise sharply in the coming days and weeks.

Sami said: “It’s going to get worse and worse at a very fast rate.”

More than 10,000 people are now stuck in squalid conditions on the Greek side of the Greek-Macedonian border, and about 200 of them have now decided to apply for asylum in Greece due to the decreased likelihood of an easy onwards route through Europe, coupled with the miserable conditions in which they now find themselves.

Others still hold out hope of moving northwards, with a group of bedraggled asylum-seekers dressed in oversized anoraks holding up a German flag on Wednesday, signalling that they still hoped to get to Germany.

Gemma Gillie, a spokesperson for Doctors Without Borders who is working at the border, said: “It’s unbelievably grim. There’s been torrential rain all day and all night.”

Additional reporting: Alberto Nardelli