Eleven children trapped on Greek islands will be flown to Luxembourg next week, the first of a European Union migrant relocation scheme that highlights the uncertain fate of thousands.

The group will leave Chios and Lesbos for Luxembourg as part of an EU voluntary effort to help the most vulnerable quit Greece’s desperately overcrowded refugee and migrant island camps.

They are expected to be the first to move since eight member states and Switzerland pledged last month to take in 1,600 unaccompanied minors.

“They are boys and girls all under the age of 12 and will fly out next Wednesday,” said Manos Logothetis, the Greek migration ministry’s general secretary. “This is a crucial first step, the start of a process that we hope can set an example,” he told the Guardian.

“In an ideal world they would leave tomorrow but there is the issue of getting through bureaucracy that is there to protect the children, meeting the criteria set by the member states and, of course, coronavirus.”

The pandemic has complicated relocation plans, with flights cancelled and restrictions on the movement of officials working with refugees. One volunteer country, Croatia, lost a building it had planned to house the children in last month’s earthquake.

The virus has also required extra medical tests being conducted on the children in addition to those needed to help check their age. European commission officials, who are co-ordinating the scheme, have been urging recipient countries to carry out tests on arrival to avoid delays.

Greece’s centre-right government, which has itself described the Aegean island facilities as “ticking health bombs”, has been pushing for resettlement of the children since September.

In an interview with the Guardian last month, the prime minister, Kyriakos Mitsotakis, said: “We sent out a letter to all the member states and got zero response. We’ve been pushing very hard for a long time on this issue.”

On Wednesday, Berlin said it was willing to accept 350-500 children “in the next few weeks”, 50 of whom would be taken as a matter of urgency. But Birgit Sippel, a German Social Democrat MEP, who sits on the European parliament’s home affairs committee, said the delay in Germany fulfilling its pledge was the result of “a political game” and reluctance among Christian Democrats in the governing grand coalition to act. Describing the number of 50 as “ridiculous”, she said it did “not [send] a strong signal regarding solidarity … from one of the biggest countries in Europe”.

Even if the pandemic had caused problems with organising flights, the German government had, she pointed out, repatriated EU travellers from around the world. While welcoming the decision, Greek officials said the process would probably be further complicated by Berlin’s demand for the unaccompanied children to be exclusively girls below the age of 14.

“Coming up with the perfect match isn’t easy,” said one official.

At the end of February, Unicef counted 5,463 unaccompanied migrant children in Greece, including 1,752 living in overcrowded reception centres on the islands. Since that date the number is likely to have increased, as people have continued to arrive either seeking asylum or better prospects. More than three-quarters of the unaccompanied children are from three countries: Afghanistan (44%), Pakistan (21%) and Syria (11%).

Children huddle under blankets after arriving by dinghy on a beach on Lesbos. Photograph: Costas Baltas/Reuters

The UN children’s agency is urging volunteer member states not to impose conditions on the children they accept, but instead to follow criteria based on need, such as the child’s age, health and any disabilities.

Aaron Greenberg, regional adviser for child protection at Unicef, said the organisation was concerned that host countries could apply sub-criteria, such as taking in only girls, under-14s or certain nationalities, which would be a problem as the majority of unaccompanied children are boys aged between 14 and 18.

“We need collective action in supporting Greece to handle this situation over the medium term,” Greenberg added. “Migration levels have ticked down, but it’s not over. We are still seeing a large number of unaccompanied children coming through. We are relieving stress, but the stress could build back up again. We need a comprehensive European agenda that goes beyond the emergency.”