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The incident took place in the city of Salvador hours after Uruguay had beaten Nigeria 2-1 in a Confederations Cup match at the city’s new $350 million World Cup stadium.
Protestors threw stones at the minibuses and broke a window at the Sheraton hotel, which is hosting FIFA delegates, the Globo Esporte news portal said.
It was not clear whether any FIFA officials were in the vehicles at the time.
Video posted online appears to show broken windows on the abandoned buses but no serious damage.
Hundreds of thousands of Brazilians have taken to the streets over the past week.
The protests were initially directed at bus fare rises but are increasingly focused on the $13 billion cost of the World Cup and similarly lavish expenditure on the 2016 Olympics in Rio de Janeiro.
In Sao Paulo, organisers called for a festive demonstration to celebrate that the fare hikes were rolled back the day before. It was estimated that 300,000 people thronged the city streets.
In the capital Brasilia, security was reinforced around the National Congress after the social network of “Wake up, Brasilia!” called for rallies – the network boasts 55,000 members.
Rousseff has postponed a state visit to Japan that was scheduled for next week, officials at the presidential palace of Planalto said Thursday.