Venter is an auditor whose company was contracted by Bosasa. Last year, Bosasa changed its name to African Global Operations.
The affidavit, which News24 has seen, was commissioned in December 2017.
Ramaphosa said he had become aware of the issue some time ago, and had questioned his son on the matter.
Venter's affidavit details that he was instructed by Bosasa/AGO CEO Gavin Watson to make a payment of R500 000 into an attorney’s trust account in October last year.
"My son has a financial consultancy business, and he consults for a number of companies. One of those companies is Bosasa. I asked him at close range whether this money was obtained illegally or unlawfully," Ramaphosa said.
According to the president, his son produced a contract between himself and Bosasa.
"He is running a clean business… if it turns out their was any irregularity or corruption I will be the first, I assure you Mr Maimane, I will be the first to make sure he becomes accountable. I will take him to the police station myself," Ramaphosa said.