Russia’s president Vladimir Putin has spoken to his South African counterpart Cyril Ramaphosa amid a diplomatic storm over a US claim that Pretoria covertly sent arms to Moscow.

The rand fell to a record low against the dollar on Friday after South Africa engaged in an extraordinary dispute with the US, one of its biggest trading partners, over the claim that weapons and ammunition were placed on board a Russian ship that docked off Cape Town last year.

Ramaphosa’s African National Congress accused the US of a “reckless” breach of diplomatic protocol over the claim, made by the US ambassador Reuben Brigety on Thursday.

The Kremlin appeared to exploit the situation on Friday, announcing that Putin and Ramaphosa had spoken and “expressed their intention to further intensify mutually beneficial relations”. Putin had outlined “the destructive line of the Kyiv regime”, the Kremlin said.

The dispute has highlighted the struggle of the west to persuade countries in Africa, Asia and South America to support Ukraine in the conflict with Russia, or at least remain neutral.

Brigety on Thursday said South Africa had placed arms on the Lady R, a vessel owned by a Russian fleet company, in December. He said senior US officials had “profound concerns” about the incident, which “does not suggest to us the actions of a non-aligned country”.

The US accusation has sparked political turmoil in South Africa and roiled its financial markets. After branding the claim “reckless”, the ANC statement was withdrawn quickly and without explanation, underlining the state of confusion that has been created by the diplomatic incident.

Ramaphosa’s government was blindsided by the US warning and was unable to deny the allegation but announced an inquiry.

At stake in the diplomatic storm is South Africa’s preferential access to US markets through the African Growth and Opportunity Act, which allows specified African nations to export goods duty-free.

South Africa’s participation was already in jeopardy over US criticism of signs that Pretoria had sought closer ties with Russia since its full-scale invasion of Ukraine.

South Africa’s foreign ministry on Friday said it had summoned Brigety and he had “admitted that he crossed the line and apologised unreservedly”.

US officials did not confirm South Africa’s version of events but appeared to try to de-escalate tensions. In a tweet, Brigety said he had spoken to foreign minister Naledi Pandor and “was grateful for the opportunity to . . . correct any misimpressions left by my public remarks”.

US secretary of state Antony Blinken also spoke with Pandor on Friday, according to a short US account of the call that made no mention of Russia or Ukraine.

“Secretary Blinken underscored the importance of the US-South Africa strategic partnership and reiterated co-operation on shared priorities, including health, trade and energy,” a spokesperson said.

Ramaphosa recently sent Sydney Mufamadi, his national security adviser, to the US to explain South Africa’s position on the war and preserve its US trade access.

Cameron Hudson, a former CIA official and senior associate with the Center for Strategic and International Studies, said relations between the US and South Africa had collapsed to their “lowest point since apartheid”. He accused South Africa of “a fundamental hypocrisy . . . declare your neutrality but in reality you’re anything but neutral”.

South Africa’s defence minister said last year that the Lady R, which began its journey in the Russian Black Sea port of Novorossiysk last October, had delivered a consignment for its own defence forces, but it never disclosed what may have then been loaded on to the vessel for the return trip.

The ANC is also under domestic pressure to explain the incident, given the economic stakes.

“Our government’s lack of transparency on allegations of armament supplies to Russia . . . has brought South Africa very close to a chain of events that will spark significant economic hardship for our nation,” said Wayne Duvenage, chief executive of the Organisation Undoing Tax Abuse, a South African transparency watchdog.

“The authorities just need to tell us if anyone in government authorised the loading and supply of whatever it was on to the Lady R and, if so, whether the inventory included armaments and/or ammunition.”

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