FENAPAF president Rinaldo Martorelli said he believed he could obtain last-minute court injunctions to stop matches from being played if FIFA did not agree to stage matches at cooler times of the day.
He said Brazilian legislation protecting workers' health would favour his cause.
"I think we can stop all the opening games in the championship which have been arranged for those kick-off times, which will cause huge disruption," he told Reuters on the sidelines of an international football conference.
Martorelli warned that he would delay legal action until the last possible minute so that World Cup organisers would not have time to get the ruling overturned.
The use of a last-minute court injunction, known locally as a "liminar", is a regular feature of all walks of Brazilian life.
In May, a judge issued an injunction ordering Brazil's friendly match against England at the recently-refurbished Maracana stadium to be suspended, four days before it was due to be played, on safety fears.
The Rio de Janeiro state government managed to get the ruling overturned, although it caused severe embarrassment and uncertainty.
"If we can sit down with FIFA and they accept our proposals, the problem is resolved," said Martorelli.
"If not, they will have to wait until the day that the players go onto the pitch, because the police and a justice official will be waiting, there will be no game."
"It won't give them time to recover, they know it's a risk that they are running...I can go to any court in the country."
Although the World Cup will take place in southern Brazil's winter, tropical conditions will prevail in the northern part of the country where Salvador, Recife, Fortaleza, Natal and Manaus will all stage matches.
Two matches in each of Natal, Salvador and Recife have been scheduled for 1300 local time plus one in Fortaleza. There will also be two 1500 kick-offs in Manaus, at the heart of the Amazon rain forest
FENAPAF said it had staged experimental matches at those times in Manaus and Fortaleza to study the effects on players and was due to issue the results in the next few weeks.
"The constitution and law favours preventative measures to protect workers' health," said Martorelli, adding that he had weekly calls from Minister of Sport Aldo Rebelo over the issue.