By Daniel Schweimler
BBC South America correspondent
Bolivia's President, Evo Morales, has held an emergency cabinet meeting to try to tackle the violence that has rocked the city of Cochabamba.
The two groups were armed with stones, baseball bats and machetes
At least two people have been killed and hundreds injured in the clashes.
The city is calmer now, with the military guarding the airport, bridges and key buildings.
But the conflict - between supporters of the local governor and coca leaf growers who back the president - is by no means over.
Mr Morales said there would be justice but he pleaded with his followers not to seek revenge after the two demonstrators were killed in the clashes with police and opponents.
He called an emergency cabinet meeting after rushing back from Nicaragua, where he had been attending the inauguration of President Daniel Ortega.
Supporters of Mr Morales had been demonstrating in Cochabamba for several days, calling for the resignation of the state governor, Manfred Reyes.
Mr Reyes is one of several state governors calling for more autonomy and greater distance from Mr Morales's radical central government.
Those protests turned violent when supporters of the governor organised a counter-demonstration and the two groups, armed with stones, baseball bats and machetes, clashed.
At least two people were killed and many more injured. Several hundred soldiers have been transferred to the city to guard the airport, bridges and key buildings.
The conflict in Cochabamba is a localised version of the divisions in the rest of Bolivia.
Mr Morales came to power a year ago with a radical plan to alleviate poverty in South America's poorest country. He has nationalised the energy industry and is trying to redistribute land.
The large indigenous community generally supports him; the business and non-indigenous population is generally against, with the divisions in Bolivia growing ever wider.