At least one person was killed in a related shooting.
The conflict is embarrassing for President Dilma Rousseff as her administration mounts a global public relations exercise to brush up the Latin American country's image before the FIFA World Cup next year and the 2016 Olympics.
The government is also anxious to avoid the indigenous people's protests becoming part of the ongoing agenda of issues pursued by Pope Francis or the Vatican in this largely Catholic country.
The government has faced criticism for its harsh treatment of inhabitants of 'favela' slums in Rio de Janeiro and other cities.
Analysts say the grievances of slum dwellers and indigenous communities risk becoming increasingly intertwined with organized crime activities, including a multibillion-dollar narcotics trade, alcohol-related crimes and people trafficking.
In indigenous communities poverty-related problems are heavily mixed with cultural and religious issues amid claims both property developers and government agencies have ignored those communities' pleas for ancestral land rights.
The indigenous grievances came to a head as activists from indigenous groups overran agricultural and other land. Farmers' representatives called for a tougher government response to protect their properties from indigenous campaigners.
Justice Minister Jose Cardozo launched a series of talks to try to placate indigenous representatives who want rights over land they claim as ancestral and sacred and a significant say in the building and operation of new hydroelectric dam projects.
Indigenous representatives say they are frustrated by the failure of previous ancestral land settlements, which collapsed due to lobbying of the federal and state governments by influential landowning Brazilians of non-indigenous -- mostly European -- ancestry.
The biggest ongoing dispute involves the Belo Monte dam complex on the Xingu River, which indigenous leaders say will devastate large tracts of their ancestral territories. The government says the Belo Monte project is essential to its master plan for staying ahead of a future surge in the nation's demand for electricity.
Reconciliation attempts involved the government transporting 144 Munduruku Indian leaders aboard air force planes to Brasilia for talks. It's not clear yet if the initiative was successful.
Guarani and Kaingang Indians rioted in the Rio Grande do Sul state and blocked roads, arguing previous agreements on their land rights had been obstructed by influential landowning lobbyists.
Officials say the government is keen to avoid a further deterioration.
"We must avoid radicalizing a situation that goes back a long way in Brazilian history. We're not going to put out the flames by throwing alcohol on the bonfire," Cardozo told reporters.
Critics say that congress is overpopulated with vested interests who do not want to give in to indigenous community leaders' demands. Neither do those vested interests want the government to stop building new dams and clearing forests for housing and industry.
Violence has flared frequently and caused at least one death in Mato Grosso do Sul and numerous injuries in other clashes. The death was reported after a shooting incident that indigenous Terena Indians blamed on powerful opponents. There were no immediate reports of arrests.
Brazil says its indigenous land policy is one of the most enlightened in the Western Hemisphere. While that may be so, critics say implementation has been slow. Farmers of European descent argue they cannot be displaced from lands they have inhabited and developed over more than 150 years.
Rousseff's senior aides continued talks with various indigenous representatives amid fears the next flashpoint could be around the Tapajaos River area in the Amazon Rainforest. Current plans call for the construction of a dozen dams on the river, a major tributary of the Amazon river.