Dozens of demonstrators, many of them striking teachers and postal workers, carried banners saying 'FIFA Go Home'.
Some made it into the Pantanal Arena and then tried to invade a news conference held by Jerome Valcke, FIFA's general secretary.
Security pushed the protesters back and the event went ahead as planned.
"People are free and (protests) are part of democracy," Valcke told reporters, before praising Cuiaba's preparations for the tournament.
Valcke, who is in Brazil to check on progress in Porto Alegre and Cuiaba, two of the 12 host cities for the tournament finals, was booed, as were the local mayor and state governor.
Two of Brazil's former World Cup winners, Ronaldo and Bebeto, both of whom are on the 2014 local organising committee, were also booed.
The protests come less than four months after millions of people took to the streets in many Brazilian cities to demand more spending on infrastructure and better quality public services during the Confederations Cup.
In several cases, demonstrators tried to reach the stadiums hosting matches but were beaten back by riot police.
The protests are a serious worry for FIFA, who are hoping for a stress-free tournament next year.
- Sports & Recreation
- Jerome Valcke