The decision affects about 20 children who come to Sweden via Greece every year, according to a report by Sveriges Television.
Several weeks ago the UN refugee agency UNHCR asked all EU countries to halt deportations to Greece. According to UNHCR the asylum process in Greece isn't legally secure.
The Migration Board sent a delegation to Greece to investigate that country's asylum process.
“We could found that the asylum system fulfilled the conditions required by the Dublin Convention. But when it comes to children, there is a risk that they can be locked up for up to three weeks. We haven't received any acceptable reasons for it, and that is why we're stopping” the deportation of children to Greece, said Migration Board head Dan Eliasson to the TT news agency.
Tuesday's decision does not apply to adults.
“The delegation had a random selection of 25 cases to investigate. Each of those cases had been heard. So we don't have any proof that adults won't have their cases tried in Greece,” said Eliasson.
In March, the Migration Court in Skåne stopped the deportation of an adult Iraqi male to Greece.
The Board appealed the decision to the Migration Court of Appeal, which recently sent the case back to the lower court for a new hearing.
“The Migration Court of Appeal's practice is clear. We can't stop deportations to Greece simply because they have lousy conditions in their reception centers, such as dirty mattresses, poor toilets, and sometimes no living quarters whatsoever. Such things aren't grounds to stop deportations within the EU,” said Eliasson.