(AFP) - South Africans were left angry and baffled on Friday after the United States accused their country of secretly shipping arms to Russia, a charge that triggered both a government rebuke but also the announcement of an inquiry.

US ambassador Reuben Brigety on Thursday said Washington was confident weapons and ammunition had been laden onto a Russian freighter that docked at a Cape Town naval base.

The explosive remarks drew an angry response from President Cyril Ramaphosa, who did not deny the charge but said a retired judge would lead an investigation into the matter.

They were also seized on by the Kremlin, which on Friday said Russian President Vladimir Putin has agreed to deepen ties with Ramaphosa.

South Africa has been walking a diplomatic tightrope over Russia's invasion of Ukraine, which it has refused to condemn, saying it prefers dialogue to end the war.

The country has strong economic and trade relations with the United States and Europe. Trade with Russia is much smaller, but Pretoria has ties with Moscow dating back decades, to when the Kremlin supported the ruling African National Congress (ANC) party in its struggle against apartheid.

The announcement of a probe was welcomed by the United States but met with ridicule and bewilderment at home.

"It perhaps points to a South African president who simply is unaware of what is happening effectively under his nose," political and economic analyst Daniel Silke told AFP.

The Lady R, a cargo vessel under western sanctions flying a Russian flag, docked at South Africa's largest naval base in December, officially to offload an old order of ammunition.

But Brigety said intelligence showed weaponry was loaded onto the vessel before it headed back to Russia.

"Did we or didn't we? And if we did, shouldn't the president know?" Bongani Bingwa, host of a popular morning radio show, wrote on Twitter.

Others quipped that the government appeared to be setting up inquiries for everything.

South Africa's foreign ministry said late Friday that the US envoy had been summoned and he had "admitted that he crossed the line and apologised unreservedly to the government and the people of South Africa".

"South Africa is known globally for having one of the most stringent processes when selling arms to other countries," it said.

Brigety tweeted that he was "grateful" to speak with South African Foreign Minister Naledi Pandor to "correct any misimpressions left by my public remarks".

The State Department also said that Secretary of State Antony Blinken had "underscored the importance of the US-South Africa strategic partnership" in a call with Pandor.

- 'Disingenuous' -

The deadline for the latest investigation has not been revealed nor who will lead it.

Khumbudzo Ntshavheni, a minister in the president's office, told local media South Africa "cannot be bullied by the US" and would follow a "time frame that is suitable for us".

If confirmed, the shipment would mark a break from South Africa's professed neutrality over the conflict in Ukraine.

The foreign ministry on Friday said there was no record of any approved arms sales to Russia during the period in question but the probe would shed light on the case.

"There should be nothing to investigate," Kobus Marais, a lawmaker with the main opposition party, the Democratic Alliance (DA), told AFP.

"The president as the commander-in-chief and the minister of defence should know exactly what happened," he said.

"It's disingenuous of them to suggest they're innocent and just bystanders."

- 'Economic suicide' -

The Kremlin meanwhile said Putin and Ramaphosa "expressed their intentions to further intensify mutually beneficial ties in various fields" during a call.

The quarrel has heightened concerns about South Africa's ailing economy, with analysts saying the country, facing near zero growth and contracting demand, has much to lose from a fight with Washington.

The rand dropped sharply against the dollar, reaching its lowest point in three years on Thursday.

Afrikaans rights group AfriForum said the government was "leading South Africa to economic suicide" by siding with Russia.

Some worry the United States could kick the country out of the African Growth and Opportunity Act (AGOA) -- a deal granting duty-free access to the US market for products from sub-Saharan nations that comply with standards on rights and democracy.

South Africa is the largest beneficiary of the agreement, which was worth $21 billion to the country's economy last year, according to the US ambassador.

© Agence France-Presse