Arsene Wenger, who is FIFA's chief of global football development, has initiated plans for a more regular World Cup.
The proposal has caused intense controversy in recent weeks with former players and current coaches debating the sustainability of changing the current World Cup format.
Motsepe, speaking in his capacity as CAF president on a trip to Ghana, threw his backing behind FIFA's proposal.
"One of the biggest beneficiaries of football every two years is the developing countries," Motsepe said to the media.
"My job is to make sure that African football grows and succeeds.
"Side by side with the Super League is to have a World Cup every two years. African football must be put in a fundamental position to benefit financially."
Motsepe also backed calls for an African Super League which he said would financially benefit the continent.
"The super league for Africa is a new competition because all of those other competitions are locked into agreements and the money they get is not enough.
"There has to be fundamental changes in how we do things in football so that African football can be noticed across the world. We do not want aid from anybody. We can work on our own and that’s what I am here to do"