The group, including teachers and postal workers and backed by students, invaded the pitch at the Arena Pantanal, one of the 12 venues which will host World Cup matches next year.
Brazilian broadcaster Globo showed the 50-strong group booing as Valcke continued his latest visit to the host nation ahead of a visit to organisers in Rio on Thursday.
A second protest marred a visit by Valcke, Brazilian Sports Minister Aldo Rebelo and local organising committee representatives and former Brazil stars Ronaldo and Bebeto to an urban mobility project.
Earlier, Valcke stressed the World Cup would go ahead using all 12 venues as scheduled despite lingering doubts as to whether all would be ready by a December deadline.
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"For last time. The Brazil #WorldCup WILL be played in 12 host cities, according to match schedule announced Oct 2011," Valcke tweeted, adding he had "full commitment" from local authorities that Cuiaba would be ready.
The Cuiaba stadium, costing some $245 million, is 85 percent complete.
One of the elements holding up the stadium project has been a row over the cost of seats, with an initial blueprint thrown out at the insistence of state and federal authorities, Globo reported.
Valcke, who Monday in Porto Alegre said his visits were a means of keeping up the "pressure" on Brazil to be ready for next June, said the 44,000 seater arena would nonetheless be ready by a December 20 deadline.