This comes as SARS is under heightened scrutiny after collecting about R30bn less than had been projected in 2016, which the tax agency blamed on economic factors. But corporate tax went up by R6.5bn over the same period.
Ngoepe said on Sunday that his office conducted two categories of investigations - Category A, which emanates from complaints by individuals or companies; and Category B, which probes "systemic problems" or issues at SARS.
An investigation into systemic problems requires approval from Gordhan, while complaints from individuals about their tax matters falls squarely into the mandate of the tax ombudsman.
Ngoepe said he had submitted a request to the finance minister last week to launch a broader investigation into issues at SARS. He is awaiting a reply from the finance minister.
"If you are getting a lot of category A complaints, which tells you there is probably something wrong with the SARS system, then you begin to say 'maybe let's look at the system'.
"I have only submitted ... my request for approval so I can investigate SARS's systemic problems relating to alleged delayed refunds of monies, which should be paid back to taxpayers." Ngoepe said he had received several complaints about the delayed payments of refunds and felt that he had "no choice" but to ask for permission to launch a probe.
"Such complaints were so many that it would have been irresponsible of me not to approach the minister fora category B investigation," he said. Complaints about the delayed payment of refunds were not uncommon, Ngoepe said. However, "this time around, there had been a noticeable increase".
He said he would continue investigating the individual complaints he received, but his hands were tied on a broader, systemic probe, pending approval from Gordhan. The Treasury and SARS could not confirm on Sunday whether it had received Ngoepe's request.
On Friday, SARS hit out at Judge Dennis Davis, the chairman of the Davis Tax Commission, saying it had lost confidence in him following comments he had made at a conference last week about perceptions about SARS's capacity.
The committee's objective is to assess SA's tax policy framework and its role in supporting the objectives of inclusive growth, employment, development and fiscal sustainability.
SARS said it had written to Gordhan, asking that Davis be removed from the committee. Davis would not be drawn into a public spat with the tax agency and said he had responded to SARS and asked to meet its commissioner, Tom Moyane.
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