Writing in his programme notes ahead of Leeds' clash with Chelsea on Wednesday, the outspoken 81-year-old claimed the possibility of staging the sport's worldwide showpiece during the Middle Eastern winter would do "irreversible financial damage" to domestic football.
FIFA came under heavy criticism in December 2010 when they announced Qatar as hosts for 2022 ahead of rival bids from Australia and the United States and despite concerns over the extreme summer temperatures experienced in the Gulf.
The world governing body later mooted moving the finals to winter, but Bates dismissed that suggestion and said Qatar should never have been chosen.
He wrote: "There have always been suspicions about staging the World Cup there.
"[FIFA president] Sepp Blatter claimed by going to new countries it is spreading the word and helps take football to a much wider audience, but Australia, who lost out, has a much higher population of over 22 million, compared to Qatar's approximate 1.8 million.
"The climate in Qatar in summer often exceeds 100 degrees, but now the suggestion is that it be switched to winter.
"That is nothing compared to the irreversible financial damage it would do to domestic football. This madness must be stopped in its tracks.
"The Association of European Leagues, the FAs and domestic leagues should join a common cause and say enough is enough."
He added: "If FIFA persist with this scheme, they should collectively boycott the event and not make their players available."
Bates went further in his tirade, urging national associations to end their membership to FIFA altogether.
He wrote: "The ultimate sanction would be to resign from this incompetent organisation and see them collapse."
FIFA was not the only organisation to feel Bates's wrath, with UEFA also coming in for criticism.
The former Chelsea owner is particularly unhappy with plans to hold Euro 2020 at cities throughout Europe.
He added: "This could mean the games are staged anywhere from Dublin to Moscow, Belgrade or even Jerusalem.
"The logistics of implementing this idea would be horrendous.
"Both UEFA and FIFA speak with forked tongues. They say clubs should reduce the size of domestic competitions to reduce players' fatigue, while at the same time increasing international fixtures, including fatuous friendlies, all for profit."