The Reserve Bank said on Friday it had not given banks any instructions on their relationships with KPMG as a result of a scandal involving the auditing firm.
Sources told Reuters last week that the central bank had told top South African lenders they cannot fire KPMG, because this might undermine financial stability.
"The South African Reserve Bank would like to state categorically that it has not instructed banks on what steps they should, or should not take, with regards to their contracts with KPMG," the central bank said in a statement.
KPMG sacked its South African leadership last month after it said it had found work done for companies owned by the Gupta family, who are close friends of President Jacob Zuma, "fell considerably short" of its standards.
The Guptas and Zuma have denied any wrongdoing.