Allegations that the Alexandra Renewal Project (ARP) funds were misappropriated are false, Gauteng MEC for Human Settlements Lebogang Maile said on Sunday.
Maile said allegations that funds were misused more than a decade ago were made "without a shred of evidence".
He added that no single person could be held accountable for the entire R1.3bn project.
"It should be stated here that the said R1.3 billion was never a ring-fenced amount where a particular individual or official was responsible. This amount was a total sum of contributions that were going to be made by all spheres of government as well as by all provincial departments."
Maile said the ARP was one of four renewal projects in Gauteng. The projects were part of eight urban renewal programmes in the country.
The R1.3bn budget was mean to be estimated for a period of seven years.
"Money was then spent in various projects including human settlements and bulk infrastructure," he said.
Johannesburg mayor Herman Mashaba has ordered an investigation into ARP alleging there was corruption in the implementation of the project.