Stone-throwing migrants clashed with police at the Moria detention centre on the Greek island of Lesbos, shortly after the Dutch and Greek migration ministers toured the former army camp.
On Tuesday plumes of smoke billowed from the compound that Pope Francis visited only 10 days ago.
A police spokesman said garbage bins in a wing for young migrants had been set on fire and the unrest spread from there.
Aid workers said tensions had been building in the camp for days but it was unclear what triggered the unrest in the centre, which came soon after a visit by the Dutch and Greek migration ministers, Klaas Dijkhoff and Yiannis Mouzalas.
Refugees and migrants have been held at the hillside detention centre under terms of a March 20 deal between the European Union and Turkey to stem the migrant flow into Europe.
It stipulates that migrants who do not qualify for political asylum must be returned to Turkey.
"Riot police are conducting an operation in and out of the camp at the moment," the police spokesman said.
Pope Francis and Ecumenical Patriarch Bartholomew, the Istanbul-based leader of the world's Eastern Orthodox Christians, met migrants begging for help as they toured the Moria camp on April 16.
The Roman Catholic pontiff took 12 Syrian refugees, who were living at another open-air camp on Lesbos back to Rome.
Official data showed there were 4,313 refugees and migrants on Lesbos on Tuesday.
The vast majority of them are held at Moria.
