Violence in the Puno region started when about 1,000 people were prevented from breaching a security fence around the international airport in Juliaca.
The protest was part of a two-day strike over a silver-mining contract given to a Canadian corporation.
The government cancelled the project as the protests were going on.
Demonstrators feared that it would increase pollution, while bringing few benefits to the local population.
Locals v multinationalsFlights were cancelled during the protest, stranding hundreds of tourists who had been visiting the town on the shores of the world's highest navigable lake, Lake Titicaca.
The protesters attempted to storm Juliaca airport twice.
They later attacked a police station in the nearby town of Azangaro, Interior Minister Miguel Hidalgo said, adding that police there were in a "difficult situation".
The BBC's Dan Collyns in Lima says the Puno region on the border with Bolivia has been in the grip of a generalised protest against all mining activity for more than a month.
In May, indigenous Aymara protesters blocked roads between the two countries for three weeks.
The disputes over natural resources pit poor locals against multinational companies, our correspondent says.
The social conflicts have come to characterise the outgoing government of President Alan Garcia, with critics saying he often took the side of the large companies, he adds.
Incoming President Ollanta Humala also has promised to bring an end to such disputes.
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