The U.S. ambassador said on Thursday he was confident that a Russian ship under U.S. sanctions took aboard weapons from the Simon's Town base in December, suggesting the transfer was not in line with Pretoria's stance of neutrality in Russia's war against Ukraine.
Brigety was summoned on Friday by the South African foreign ministry, which "expressed the government's utter displeasure with his conduct and statements made yesterday" a statement from the ministry said.
Western diplomats were alarmed at South Africa carrying out naval exercises with Russia and China this year, and at the timing of a visit by Russian Foreign Minister Sergei Lavrov.
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 U.N. resolutions on the war.
Russian President Vladimir Putin on Friday had discussed the conflict in Ukraine in a phone call with South African President Cyril Ramaphosa, the Kremlin said.
Ramaphosa's office said on Thursday that an inquiry led by a retired judge would look into the U.S. 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 702 radio.
He did not say whether or not an unapproved shipment had left South Africa.
South Africa's defense department said on Friday it would give its side of the story to the government's inquiry.
There was no immediate response from the U.S. State Department.
White House National Security Council spokesman John Kirby on Friday declined to get into the specific allegations against South Africa, but reiterated Washington's position about any country aiding the Russian war effort.
After leaving Simon's Town, Refinitiv shipping data showed the vessel, the "Lady R," sailed north to Mozambique, spending Jan. 7 to 11 in the port of Beira before continuing to Port Sudan on the Red Sea.
It arrived in the Russian port of Novorossiysk on the Black Sea on Feb. 16, the data showed.
The United States placed the Lady R and Transmorflot LLC, the shipping company it is linked to, under sanctions in May 2022 on the grounds the company "transports weapons for the (government of Russia)."
Opposition members called on South Africa's government at the time to explain what the "mysterious" ship was doing at the naval base.
"Evidence suggests that over the last two nights there was unusual activity in the harbour with on-board cranes offloading cargo from the Russian commercial vessel onto trucks," said Kobus Marais, who heads the opposition Democratic Alliance's defence portfolio, in a statement on Dec. 8, 2022.
There were also trucks transporting containers in and out of the naval base, which is common but not at night, said Marais, adding that the trucks were protected by armed personnel.
South Africa's presidency said the issue had already been discussed with U.S. officials who had agreed to let an investigation run its course, and that no evidence had yet been provided by Washington.