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.

The band were named best international artists, beating Eminem, Coldplay and Pharrell Williams.
They also performed Steal My Girl at the ceremony in Sydney.
Katy Perry and 5 Seconds Of Summer were also on red carpet selfie duty... to the max.
See Liam trying to look happy, but not massively succeeding, in this Vine video (posted by 18styles).
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Romania face action after fans set off fireworks and threw objects, with Albania accused of the same offences in addition to allowing a pitch invasion.
The charges mean that eight of the 24 teams competing in the tournament are the subject of disciplinary probes.
Albania won the Group A match 1-0 to maintain slim hopes of progressing while eliminating Romania.

Cavendish, 30, is looking for more qualification points at the event in Germany from 28-29 August in order to compete for GB in the omnium in Rio.
Coach co-ordinator Iain Dyer said: "He made a very promising start back on the track in Derby and he'll be looking to continue building on that form."
Cavendish won the Madison with Bradley Wiggins at the Derby Revolution.

Drifters was made in 1929 by acclaimed Scottish documentary-maker John Grierson.
It shows fishermen harvesting shoals of herring off Scotland's east coast.
East London-born sound artist Jason Singh will provide vocal sound effects during screenings of the film in Lerwick, Helmsdale and Anstruther.
The tour, called Following the Fleet, is supported by the National Lottery through Creative Scotland and also by Film Hub Scotland, which is part of the British Film Institute's Film Audience Network.
Between 31 August and 18 September, the film and performances will be held at venues in Baltasound and Lerwick on Shetland, Stromness on Orkney, Helmsdale in Sutherland, Aberdeen and Anstruther.
Singh, who will also deliver workshops on beatboxing and other sound effects for secondary school pupils at the venues, said: "I'm really excited about the Following The Fleet tour.
"I am keen to see what people will make of a live beatboxed score to a silent film.
"I'm also really looking forward to running workshops as it will give people the opportunity to explore their own voices in new ways and it will also give me the chance to meet, share and explore with new communities and cultures."
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.
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