The US ambassador to South Africa Reuben Brigety said on Thursday he was confident a Russian ship under US sanctions took aboard weapons from the Simon's Town base in December.
South Africa is one of Russia's most important allies on a continent divided over its February 2022 invasion of Ukraine, but says it is impartial and has abstained from voting on UN resolutions on the war.
Russian President Vladimir Putin discussed the conflict in Ukraine in a phone call with South African President Cyril Ramaphosa on Friday, the Kremlin said.
Ramaphosa's office said on Thursday that an inquiry led by a retired judge would look into the US allegation. On Friday, a minister responsible for arms control and a foreign ministry spokesman said South Africa had not approved any arms shipment to Russia in December.
"We didn't approve any arms to Russia ... it wasn't sanctioned or approved by us," Communications Minister Mondli Gungubele, who chaired the National Conventional Arms Control Committee when the purported shipment took place, told a radio station. He did not say whether or not an unapproved shipment had left South Africa.
Brigety was summoned on Friday to meet South African foreign minister Naledi Pandor. The ministry "expressed the government's utter displeasure with his conduct and statements made yesterday," a statement said.
It said Brigety "admitted that he crossed the line and apologised unreservedly to the government and the people of South Africa."
Brigety said on Twitter: "I was grateful for the opportunity to speak with Foreign Minister Pandor this evening and correct any misimpressions left by my public remarks."
The US State Department said Secretary of State Antony Blinken had a phone call with Pandor "and reiterated cooperation on shared priorities, including health, trade, and energy."
After leaving Simon's Town, shipping data showed the vessel, the "Lady R", sailed north and arrived in the Russian port of Novorossiysk on the Black Sea on February 16.
Washington has warned that countries providing material support to Russia may be denied access to US markets.
Authorities in South Africa's opposition-run Western Cape province said they feared losing a market for exports such as oranges, macademia nuts and wine.
The US allegation over the weapons has heaped pressure on the rand currency, already weighed down by concerns over a power crisis. It struck an all-time low early on Friday before regaining some ground, but remained at its weakest in three years.
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