The deadly clashes erupted in the city of Cusco on Wednesday when riot police used tear gas to push back thousands of protesters marching towards an airport in the southern Andean region.
Many protesters were carrying sticks and throwing stones as they tried to storm the airport.
The protesters came to Cusco from the nearby province of Calca, as part of a 48-hour strike against the re-drawing of local districts.
The protesters say the new boundaries reduce the land in their province.