Three workers were killed when a crane collapsed on the grandstand, which in turn fell onto a truck, at the Corinthians Arena. Officials have named two of the victims, Fabio Luiz Pereira, 42, and Ronaldo Oliveira Dos Santos, 44.
"The board of Sport Club Corinthians Paulista hereby deeply regret the accident earlier in Corinthians Arena," the stadium owners said in a statement.
"Teams of firemen are in place. At the moment, all efforts are focused to provide full assistance to the families of the victims," the statement said. While the accident occurred during lunch hour, only 30 people were in the area, rather than the usual 1,700.
"We know the safety of all workers has always been paramount for all the construction companies contracted to build the 12 FIFA World Cup stadiums," FIFA said in a statement.
"The local authorities will fully investigate the reasons behind such a tragic accident."
FIFA president Sepp Blatter tweeted his condolences.
"I'm deeply saddened by the tragic death of workers @Corinthians arena today," he wrote. "Our heartfealt condolences are with the families."
Wednesday's collapse was the latest incident troubling the preparations for the World Cup, which begins on June 12.
A judge halted work at Arena da Baixada stadium in Curitiba last month after he determined there was too much risk of an accident. And a fire at the Arena Pantanal in Cuiabá slowed construction a month before.