Makhanya is unrepresented and has claimed he cannot afford a lawyer.
The witness said Makhanya was the principal architect on the project.
National Treasury regulations required there to be proper planning and procurement of service providers but the investigation revealed several “deviations” from these.
One was that the department of public works did not ensure that services were sourced from the approved database in circumstances where there were no emergency conditions.
She said a R2m professional fee paid to the architect, based on his letter of appointment, was not justified and that Zuma’s family had wanted him appointed because he had done work at the homestead previously.
There was no open tender or competitive bidding for the job.
She said approval of the initial budget of R27.2m was given in August 2009 but it did not include security upgrades.
Former minister Geoff Doidge gave input at meetings to prepare for the rollout of these.
The amounts increased significantly after the former regional head of public works issued the request that the project begin.
A professional team was appointed to work with Makhanya but its members were not registered as consultants and it was not clear who appointed them.
At one point, Zuma raised concerns about the progress of the project with Doidge.
When the witness alleged that Makhanya was responsible for separating public and private funding for the project, he objected.
Judge Pillay said Makhanya would be given an opportunity to cross-examine the witness later.
The hearing will continue on Tuesday. The SIU is expected to call two other expert witnesses, including an architect and a quantity surveyor.
All evidence will be heard in camera.