More than 60 people have been hurt, many of them riot police, in clashes with protesters on Lesbos and Chios over plans to build new migrant camps.
Stones were hurled at police as protests intensified at three Lesbos sites where the centres are to be built.
Greek Prime Minister Kyriakos Mitsotakis has called for calm and is due to meet the regional governor and local mayors to discuss the crisis.
Several police were also hurt on Chios, reports the BBC.
Authorities in Athens have pledged to build new centres to replace overcrowded facilities on Lesbos, Samos, Chios, Leros and Kos. The government plans to bring down the number of migrants on the islands from 42,000 to 20,000.
All five islands lie off the coast of Turkey, on a route where hundreds of thousands of migrants have tried to cross the sea on the way to Europe in recent years.
But there has been intense local opposition to the new centres.
After weeks of talks between the government and local people, the government secretly shipped construction machinery and hundreds of riot police officers to Lesbos and Chios.
Wednesday saw the second consecutive day of protests on the islands. The largest were on Lesbos and Chios.
In Lesbos, crowds attempted to approach a site earmarked for a migrant centre.
A police spokesman said more than 1,000 people were at the site and claimed they had thrown stones at officers, smashing their helmets. During the day, 43 police and 10 protesters were hurt.