Several hundred protesters have occupied some 1,800 hectares (4,500 acres) in Cauca department demanding control of the land where their relatives were killed in massacres during Colombia's five-decade guerrilla war.
The protesters, who began their occupation a week ago, threw stones and Molotov cocktails at riot police who tried to evict them, said Oscar Quintero, the mayor of the town of Corinto, where the clashes occurred.
The police responded with tear gas and stun grenades.
Colombia's indigenous peoples, who make up 3.4 per cent of the population, have been caught up at various times in the country's 50-year-old conflict, which has drawn in several leftist guerrilla groups, right-wing paramilitaries and drug traffickers.
The Colombian government has established indigenous reserves that span roughly one-third of the country, but many indigenous communities have been forced from their land by conflict over resource-rich and coca-farming areas.