Nearly 80 protesters, mostly Germans, Britons, Italians and some Bulgarians, were rounded up after allegedly throwing stones, bolts and other projectiles at riot police guarding the site on the Halkidiki peninsula, the authorities said.
The police fired back tear gas to disperse them.
Anti-mine protesters claim the project will cause irreversible harm to the environment, draining and contaminating local water reserves and filling the air with hazardous chemicals including lead, cadmium, arsenic and mercury.
Some 2,000 people had earlier taken part in the protest held by anti-capitalist group Beyond Europe near the site operated by Hellas Gold, a subsidiary of Canadian company Eldorado Gold, protest organisers said.
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The Greek leftist government this week blocked work on the goldmine over alleged contract violations.
The energy ministry said the company had failed to provide an environment-friendly gold extraction plan within a three-year timeframe as promised, and had been given another year to deliver.
While in opposition, the now-ruling Syriza party publicly opposed the investment. However, many residents support the project.
The company, which already operates other mines in the area, this week said the suspension had put 5,000 direct and indirect jobs in Greece at risk.