In some hotels featured by the Fifa-appointed agency Match, room rates will be up to five times higher during the tournament, a recent study suggests.
The board fears that "stratospheric" costs could damage the country's image.
The World Cup opening match will be on 12 June 2014, in Sao Paulo.
The board, known as Embratur, said that Match should change its policy of blocking hotel rooms and also called upon the agency to reduce its mark-up rates.
"We propose that the companies involved conduct new rounds of negotiations to lead to a restructuring of the prices,'' the board was quoted as saying in a document by the Associated Press news agency.
The board claimed: "Fifa/Match charges mark-up rates of more than 40% on the amount contracted with the hotel, something that contributes decisively to the increase of the already high rates."
However, Match said that it does not regulate room rates and that prices are set "by the hotel owners and other tourism stakeholders".
"As of yet it is totally unclear to Match Services on what criteria Embratur has been comparing rates as we have not been consulted in this matter," AP quoted the agency as saying.
It added that if hotels lowered their rates if would "readily pass the benefit of any such reduction to its customers".
The World Cup is one of the most popular sporting events and is expected to attract a large number of tourists to the host country.
According to Fifa, the 2006 World Cup held in Germany was attended by more than 3.3 million fans - with many of them flying in from all across the world.
Fifa is expecting a similar demand for the 2014 World Cup.
Brazil's tourism board said that it was concerned that if fans coming from outside the country had to pay excessive prices, it might hurt the country in the long run.
"We want to guarantee economic success and a legacy for the country that goes beyond the 2014 World Cup,'' it said.
In June, there were widespread protests in Brazil where the high cost of preparations for the World Cup was among the issues raised.
Brazil's tourism board has asked world football governing body Fifa and hotel operators to try to bring down hotel prices â€“ which have reportedly sky-rocketed for the World Cup period.