The auditor general's spokesperson, Africa Boso, said on Wednesday that Terence Nombembe would not conduct what he termed "a special investigation".
"Various impacted government departments, including the department of defence, had already instituted their own internal investigations into the matter," he said in a statement.
"[We] would study and report on the findings of these departmental investigations, if any, as part of our normal 2013/14 annual audit."
Boso said this was conveyed to Democratic Alliance (DA) MP Dianne Kohler-Barnard, who earlier said Nombembe agreed to conduct a probe into the Gupta matter.
A chartered Gupta family jet carrying 270 wedding guests made an unauthorised landing at Waterkloof Air Force Base, a national key point, last Tuesday.
The jet was moved off the base on Thursday afternoon, amid widespread criticism. The passengers were escorted to Sun City, in North West, to attend a lavish Gupta family wedding.
The politically connected Guptas own the New Age newspaper and Sahara Computers, along with several other businesses. A committee of directors general has been appointed to probe how the jet was allowed to land at the Pretoria airforce base.
They were given seven days to complete the investigation and report to Cabinet.
Kohler-Barnard asked Nombembe's office to investigate whether any unauthorised, irregular or wasteful spending occurred as a result of the Gupta's use of state resources.
The DA also wanted light shed on the chain of command for approval of the alleged expenditure and use of state resources.
Kohler-Barnard said that the auditor general's undertaking was an indication that a full-scale parliamentary inquiry should be also be launched. – Sapa