Police in riot gear threw teargas and fired water cannon at Greek islanders as they tried to prevent access to construction sites for new migrant detention centres by setting fires, hurling flares and blockading the gates.
Locals on Lesvos and Chios are worried that the centres, which would replace temporary camps with open access, will leave the islands permanently overcrowded.
Vowing to press on with the building work, authorities say closed centres will offer greater public safety and limit potential health risks, particularly given the potential spread of the coronavirus in other countries.
"It is clearly evident that matters such as the coronavirus can be dealt with swiftly and effectively in a closed facility and not an anarchic, open facility which is a health time bomb," government spokesman Stelios Petsas said.
There are currently no cases in Greece.
The authorities moved to send police reinforcements to the islands to deal with the protests, prompting more clashes as islanders tried to prevent the arrival of the ferries.
Condemning what he called a "day of shame", Costas Moutzouris, governor of the northern Aegean region, branded the deployment "extremely aggressive" and announced a decision by local authorities there to hold a 24 hour general strike on Wednesday against the actions of the central government, the Athens News Agency reported.
Witnesses said about 500 people attempted to block the unloading of heavy machinery overnight to break ground at the construction site on Lesbos.
Clashes between protesters and police broke out and fires burned on the streets and in the roadside brushland, ignited by the flares. Similar tensions were reported on Chios, where residents also say they are bearing the burden of the refugee crisis.
In addition to Lesvos and Chios, Greek authorities plan to construct closed detention facilities on Samos, Kos and Leros. The islands are close to Turkey, from where thousands of asylum seekers head to Europe each year.
Hundreds of thousands of people crossed into Europe from Turkey via Greece in 2015 and 2016 before a deal brokered by the European Union limited the flow. There has, however, been a resurgence in arrivals since September 2019.
The overcrowded Moria camp on Lesvos accommodates more than 18,000 people in conditions aid organisations say are appalling.
The conservative government has taken a markedly tougher stance towards migration compared to the previous leftist government, issuing a tender for the construction of a floating fence to deter asylum seekers arriving by sea and introducing faster processing procedures that could increase deportations.