Consulting firm Bain & Company, which was involved in the controversial SARS restructuring plan, says there was a possibility it may have been "used to further a political or personal agenda".
Bain was paid R164m to develop a new operating model, commissioned by now-suspended South African Revenue Service (SARS) boss Tom Moyane.
The model has come under fire from senior officials who testified before the Nugent Commission, for destabilising the tax service and collapsing highly efficient revenue collecting units.
"There is a growing frustration within our firm that we did not recognise the possibility that we may have been used to further a political or personal agenda," Bain said in a statement issued on Sunday.
The company last week defended its structure as it presented evidence before the Nugent Commission, saying it was meant to strengthen SARS. The company instead laid the blame for unsuccessful implementation at the door of SARS.
"We are dismayed by the way our work has been used to further a different agenda than was intended," Bain said.
The restructuring plan led to the shutting of the Large Business Centre, which has been blamed for a a major loss in revenue collection, as well as a haemorrhaging of skilled senior employees.
"In our recommendations, there was no need for any lay-offs or terminations. This didn’t turn out to be the reality when the model was implemented."
Concluding his evidence before the inquiry, Bain representative Vittorio Massone, a managing partner at the company’s Johannesburg office, was asked by Judge Robert Nugent if he wanted to apologise to South Africans for the role the company played in the destruction of SARS.
Massone only apologised to SARS employees who felt that they "might not have been treated professionally" by Bain during its interaction with them. He stated that he had nothing else to apologise for.
But in the statement, the firm said it was "deeply sorry" for how its work turned out, adding: "We wish we had known then what we do now."
The inquiry heard from numerous SARS employees that Bain did not adequately consult with them as it conducted its work, and did not consider the input of business unit leaders.
"In hindsight, as we reflect on our role at SARS, there are several places where we could have done better. We could have listened better," it said.
"We contend that this could have been avoided."
Bain initially conducted a diagnostic of SARS before proceeding with the overhaul of the operating process.
The commission consistently questioned the rationale of tampering with the operational model of a highly efficient institution which is crucial to the country's development.
Bain announced it would undertake a "deep and extensive investigation" into its work at SARS.
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