Scuffles broke out in the city of Thessaloniki, Greece's second-largest city, on Monday.
The protesters were predominantly members of the right-wing group "Sacred Band."
Meanwhile, a group of around 200 pro-refugees, known as antifa, held a counter-demonstration nearby. The latter rally was organized by the Movement against Racism and the Threat of Fascism (KEERFA).
A large number of police officers were deployed to prevent possible clashes between the two groups.
Greece has been struggling to cope with the huge number of refugees pouring into the country.
On Sunday, Greece started evacuating refugees from a major camp on the Macedonia border.
More than a million refugees, most of them taking the sea route between Turkey and Greece, crossed into Europe in 2015, creating the worst refugee crisis for the continent in decades.
The inflow prompted European Union (EU) officials to reach a multi-billion-dollar deal with Turkey whereby Ankara takes back all the refugees coming to Greece in return for billions of dollars in aid and an acceleration in talks for its long-sought membership in the EU.
Major international organizations, including the United Nations refugee agency, UNHCR, have slammed the deal, saying it violates the rights of the refugees.
Athens has used the relative calm on its border to establish centers for the deportation of refugees. Some 4,000 security personnel and asylum experts have been deployed by the government while refugees are being transported to registration centers set up on five Aegean islands.
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