SAP, along with auditors KPMG and consultant McKinsey & Co., has become entangled in allegations surrounding the Guptas, who are friends with President Jacob Zuma and have been in business with his son.
German software giant SAP has come forward, apologised and admitted wrongdoing on their behalf for the company's work in South Africa.
An internal probe by law firm Baker McKenzie found that the Walldorf-based company paid Gupta-related businesses about R94 million in commission after receiving help to win contracts with two South African state-owned companies, SAP said.
The company says investigations into Gupta-related third parties payments have not revealed any evidence of payments to any Transnet employees.
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Claims have surfaced saying Zuma was influenced by the wealthy Gupta family to appoint and dismiss ministers in accordance with their interests or to secure lucrative government contracts.
SAP will publish full findings of its investigation upon conclusion of the investigation.
The three Gupta brothers, who reportedly relocated to South Africa from India in 1993, and Zuma have denied any wrong-doing.
"We have reported misconduct to USA authorities, but we have not had any interaction with South African authorities", Fox-Martin said. South Africa's Corruption Watch has said it could report the firm to the DoJ, while the Federal Bureau of Investigation recently opened its own probe into USA links to the family, according to the Financial Times.
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"As a global company with a commitment to integrity and compliance, the past three months have been humbling for us", SAP executive board member Adaire Fox-Martin said in the statement. SAP also started disciplinary proceedings against three employees.
As result of the last few months of trouble SAP has instituted a process change in countries where the Corruption Perception Index (CPI) rating is below 50.
SAP received revenue of about 660 million rand ($47 million) and paid commissions to Gupta-related entities, SAP said.
The Guptas, whose interests include mining and media companies, are being investigated in South Africa over the appropriation of public money, known as "state capture".
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While SAP's statement initially sent shares down as much as 0.9 percent in Frankfurt trading, the stock has since rebounded, rising 0.4 percent to 95.83 euros as of 11:36 a.m. local time.