Greece, with 192 coronavirus deaths, has so far not been as badly hit as many other European countries, and there have been no deaths in the migrant camps.
Out of 40 groups currently active in camps, 22 were eliminated from a first approval phase after failing to apply by June 14, the ministry said in a statement.
"The temporary shutdown of cross-border movement within the EU will inevitably impact when and how vulnerable children in Greece are relocated to Germany, Finland and other states," a senior UNICEF official said.
Refugees from war zones are stuck in Serbia after the route to western Europe was officially closed last year.
Greece is struggling to reduce overcrowding at refugee camps on its islands, even though the flow of people is less than last year.
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