The Roman Catholic leader made the comments while meeting migrants during a visit to a basilica in Rome.
He thanked those who welcomed refugees but said that it appeared “international accords are more important than human rights”.
The American Jewish Committee said the Pope should rethink his “regrettable” reference to concentration camps.
The term “concentration camp”, which predates World War Two, is nonetheless evocative of the centres set up by the Nazis for slave labour and the extermination of millions of Jews and others.
Pope Francis told migrants at the basilica of St Bartholomew on Saturday about his visit to a camp on the Greek island of Lesbos last year.
He met a Middle Eastern refugee who said his Christian wife had been killed by militant Islamists for refusing to throw her crucifix to the ground.
The Pope said: “I don’t know if he managed to leave that concentration camp, because refugee camps – many of them – are concentration… because there is a great number of people left there inside them.”
He said the “generous people” who welcomed refugees “must bear this extra burden, because it seems that international accords are more important than human rights”.
The Pope did not elaborate, but the European Union has agreements to try to prevent the entry of migrants crossing from Libya and Turkey.
He added that he hoped the generosity of southern Italy could “infect the north a bit”.
“If every municipality in Italy took in just two migrants there would be a place for everyone,” he said.