The warning went out ahead of Friday's opening of applications for a share of the 2010 World Cup legacy trust, which amounts to R450m in total.
Jordaan, who is a vice-president of the South African Football Association and a trustee, said the money would immediately be withdrawn if it was not used for its intended purposes.
"The legacy would be used to address critical gaps in football development in all provinces," said Jordaan.
Only public organisations will be eligible for funding and the trust will subsidise projects for institutions that include SAFA, SAFA regions, SAFA local football associations, schools and universities, and NGOs that use football as a vehicle for community development.