Confederation of African Football (CAF) president Hayatou, who has twice denied corruption allegations in the last year, will head the Goal bureau which oversees funding of what is seen as one of FIFA's most important projects.
The Goal programme provides support for football development projects such as creation of youth academies, the modernisation of national association computer systems, and the promotion of women's football, futsal and beach football.
Inaugurated in 1999, it has already provided support for over 500 development projects across the world, with a total of 200 million dollars having been invested in them, FIFA said.
FIFA's website said that "for the 2011-2014 cycle, and with the approval of the Congress, FIFA's Executive Committee has set funding for each Goal project at 500,000 dollars.
"In addition each project must be submitted to the Goal Bureau for its approval."
Hayatou, who will also be in charge of the committee which oversees organisation of the football tournament's at next year's London Olympics, has been CAF president since 1987.
In May, a British parliamentary inquiry into England's failed 2018 World Cup was told that the 65-year-old from Cameroon was paid by Qatar to for their successful 2022 World Cup bid.
Hayatou said he "categorically denied allegations of corruption brought against him."
The previous November, he said he conscience was clear after the BBC's Panorama said that a payment Hayatou received from FIFA's former marketing partner ISL was a bribe.
"Personally, I know no-one can influence me," he said at the time.
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