More than 5,000 people took to the streets of Greece's second-largest city on Saturday, police said, to protest against a controversial gold mine that has frayed relations in a northern village.

Protesters carried a banner reading "Toxic dust doesn't have boundaries. No to gold mines" in Thessaloniki, while in Athens, 500 more gathered to shout slogans denouncing police brutality they allege was directed at those who have taken action against the mine.

Opponents of the venture in Ierissos, a village on the tourist-friendly Halkidiki peninsula, believe it could poison groundwater supplies in the area.

Violent resistance has broken out repeatedly since government permission to break ground on the project was granted in 2011 to Hellenic Gold, a Greek subsidiary of Canadian mining firm Eldorado Gold.

In February militants threw Molotov cocktails at the site, wounding a guard and damaging equipment.

This was followed two months later by the ransacking of the local police station in retaliation for what inhabitants saw as excessive force used in the arrest of two suspects connected with the previous attack.

More than 200 people in the region around the mine are due in court on criminal charges connected with the demonstrations, leading to accusations that the authorities have criminalised the protest movement.

Anti-mine activists claim it will poison local water supplies with mercury, lead and arsenic, but the government says the venture could create hundreds of jobs in a country with an unemployment rate of 27 percent.