Reuben Brigety claimed that a Russian ship was loaded with ammunition and arms in Cape Town last December.
President Cyril Ramaphosa's office said it was disappointed by the claims and said no evidence has been provided to support them.
The country has maintained claims of neutrality in the invasion of Ukraine.
Mr Brigety said at a media briefing in Pretoria on Thursday that Washington had concerns about the country's stated non-aligned stance on the conflict.
