At least 45 people have died after their boats sank near two Greek islands

Angela Merkel says tragedy underlines need for EU partners and countries in region to address causes of conflicts.

At least 45 people have died after their boats sank near two Greek islands, the latest tragedy on the border of a continent still riven by seemingly intractable disagreements over how to deal with its refugee crisis.

In a double shipwreck that made this month the deadliest January on record for migrants trying to cross the sea, two wooden boats sank in the eastern Aegean off the islands of Kalymnos and Farmakonisi.

Speaking in Berlin after a meeting with the Turkish prime minister, Ahmet Davutoğlu, the German chancellor, Angela Merkel, said the deaths underlined the need to ensure that immigration could happen “in a legal way”.

“Today we have heard of the terrible deaths in the Aegean. We cannot allow that between Turkey and Greece people smugglers and traffickers are running their operations,” she said, making another plea for unity on the issue.

“Deep inside, I’m convinced that the question of illegal migrants can only be solved if we first fight together against the causes ... and we as a union have a great interest in keeping Schengen together,” Merkel said, referring to the passport-free EU zone.

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Merkel denied feeling isolated by her open-door refugee policy, which has been met with fierce opposition, both domestically and regionally. Questioned on the subject, she retorted: “I don’t have that impression, not now, not ever.”

But she has faced growing criticism in Germany, particularly from her coalition ally, Bavaria’s Christian Social Union, which has repeatedly called for her to shut the country’s borders.

She has also failed so far to convince European partners to accept refugee quotas and faces repeated accusations that she triggered the flow of refugees to Europe. Refugees continue to arrive in Germany at a rate of about 2,000 a day.

They also continue to die at sea: according to the International Organisation for Migration, the deaths in the Aegean in the past 24 hours bring the total number of fatalities recorded to at least 113, more than in January 2014 and January 2015 combined, when 94 deaths were recorded – 12 in January 2014 and 82 last year.

Speaking to the BBC at the World Economic Forum in the Swiss resort of Davos, the French prime minister, Manuel Valls, said Europe could not take in all those fleeing wars in Iraq and Syria without putting the concept of Europe itself in grave danger.

Valls said Europe needed to take urgent action to control its external borders, “otherwise our societies will be totally destabilised”. Asked about border controls inside Europe, which many fear put the Schengen zone at risk, Valls said: “If Europe is not capable of protecting its own borders, it’s the very idea of Europe that will be questioned.”

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The EU is deeply divided on addressing the influx, with several countries blocking or restricting migrants from entering and resisting plans to share the burden of refugees.

Austria said this week it would introduce an upper limit and Macedonia has temporarily closed its border with Greece, leaving thousands of refugees stranded in freezing conditions along the Balkan route. Hungary’s prime minister, Viktor Orbán, who last summer built a fence at the country’s border with Serbia, said on Friday another fence should be erected on the Macedonian and Bulgarian borders with Greece.

Emmanuel Macron, the French economics minister, told an audience of business leaders that time was of the essence. “We have a few weeks to concretely deliver our options ... otherwise you have country-by-country solutions [and that will be] the beginning of the dismantling [of the EU] for sure,” he said.

Merkel, who has thrown her weight behind an EU deal with Ankara to stem the flow of refugees, has been accused by German commentators of leaving herself open to blackmail by Turkey. Brussels has pledged to provide €3bn (£2.2bn) and political concessions to Ankara in return for decisive action on border control.

But on Friday she insisted that the EU had to work closely with the countries in the region to tackle the causes of the conflicts that were forcing people to flee. Greece’s migration minister also said Brussels was crucial to easing the crisis.

“The only way to control the flow is to stop it on the coasts of Turkey,” Yiannis Mouzalas told the Guardian. “Once they are on the boats it is too late. The European Union must help Turkey and demand that it responds to its obligations. No one, with all the political will, can do it alone.”

He said the flow would continue to be “uncontrollable” if Turkey was not aided in implementing commitments to stop it.

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Turkey, which shares borders with Syria and Iraq, has close to 4 million refugees, the vast majority living in camps.

Ankara has so far seen none of the promised EU funds. Merkel promised at Friday’s meeting she would personally ensure the money was paid, despite a move by Italy to block the deal.

Davutoğlu welcomed the cooperation with Germany, saying that Turkey had spent the past few years dealing with the influx of refugees along its 4,500 mile (7,200km) shoreline on its own, including coping with the consequences of the “social instability” it had caused.

“For the last four years Turkey did everything it could without getting any support from any other country. We tried to solve the problem ourselves, but we see what happens when a terror organisation forces people out of their country,” he said.

He added that it was a mistake to see the refugee crisis as that of one nation. “It is not a German crisis, a European crisis or a Turkish crisis. Neither can we just pass this crisis on from one country to another. We have to solve this crisis together in Syria and Iraq.”

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Mouzalas, who has previously worked with migrants as a doctor with the aid group Doctors of the World, said the latest incidents proved that legal resettlement was the only way forward.

“To stop and decrease the flow we have to give these people a legal route, a safe corridor of legal resettlement from Turkey, Jordan and Lebanon to the EU,” he added. “This is about smugglers, human traffickers, international crime. If it were drugs they [authorities] would have done something. It is even more urgent now that we act to stop them because it is not drugs but people who are involved.”

After the sinking of the first refugee boat on Friday, a huge rescue operation was launched with a Super Puma helicopter, three coastal boats and fishermen all scouring the waters off the island of Kalymnos. More than 70 people survived. Divers were due to descend to the sunken wreck early on Saturday, amid fears that more people had been trapped below deck.