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US president Joe Biden’s administration is seeking to play down a rift with South Africa over the allegation that Pretoria covertly shipped arms to Russia, signalling a desire to address the dispute privately to avoid further damaging their relationship.

In a break from diplomatic protocol, the US ambassador to South Africa claimed this month that arms were placed on a sanctions-hit Russian vessel under cover of darkness in a Cape Town naval base last December, later adding that he would “bet my life” on it.

His accusation reflected deep frustrations in Washington over South Africa’s publicly supportive stance towards Moscow. Russia has cultivated strong ties with the ruling African National Congress, which the Soviet Union backed when it was in exile in the apartheid era.

But many in the US administration worry that publicly rebuking or penalising supposedly non-aligned countries, such as South Africa, over their ties with Russia risks pushing them closer to Moscow.

Officials have refused to comment publicly or privately on the details of the accusation by Reuben Brigety, the US ambassador, saying they would wait for the results of an investigation launched by South African president Cyril Ramaphosa. Two people privy to the administration’s thinking have suggested though that the ambassador had complicated matters by going public with the accusation.

South Africa’s refusal to condemn Russia’s invasion of Ukraine has irked the Biden administration. But Washington also believes Biden has a rapport with Ramaphosa and that diplomacy is the best way to handle the frayed relationship with their largest trading partner in Africa.

“Ramaphosa and the South African government have said an investigation is under way and we look forward to the results,” said a US National Security Council official.

Congress may still try to press the US government to take a harder line, analysts said. Jim Risch, the top Republican on the Senate foreign relations committee, said he shared Brigety’s concerns about South Africa’s ties with Moscow.

“The Biden administration should use existing authorities to re-evaluate the scope and scale of our current engagement with South Africa’s government,” he said.

The diplomatic spat over the Russian ship, the Lady R, reflects the delicate path that Washington has to tread as it seeks to convince reluctant members of the “global south” to back the west’s position over the Ukraine war.

Since Moscow’s full invasion of Ukraine last year the US has sought to press traditional strategic partners to at least remain neutral and to enforce international sanctions, as a way of depriving Vladimir Putin’s regime of the funds and arms it seeks to conduct its war.

In a sign of US conciliation over the issue, Brigety has said he regretted any misconceptions that his remarks created about South Africa.

Ramaphosa has identified a retired judge to head the Lady R inquiry but has yet to name that person or finalise the terms of reference for the probe, his office said this week.

His government has denied selling weaponry to Russia and suggested that if any transfer did occur, it was done by a rogue actor. The government is yet to see concrete proof for the US claim regarding the vessel, Ramaphosa’s spokesperson said this week.

Patrick Gaspard, ambassador to South Africa from 2013 to 2016 and now president of the Center for American Progress think-tank, said both sides appeared keen to de-escalate.

“There’s been a kind of reckoning with the seriousness of what it would mean to actually have ruptured relationships between the US and South Africa, who are incredibly important allies,” he said.

“There’s still serious issues here but these issues are going to be addressed across the diplomatic table,” he added.

There is, however, deep-seated antipathy towards the US inside the ANC, which has publicly accused Washington of provoking the Ukraine war. The party’s ties with Russia strengthened under South Africa’s former president Jacob Zuma, who worked closely with Moscow when he was in exile under apartheid.

Zuma, whose government became notorious for its corruption of state bodies, was a keen supporter of a bid by Russia to build nuclear plants in South Africa. The deal was cancelled by a South African court order.

“There’s a really significant portion of the South African establishment that believes the US is an antagonist of some sort,” said Michelle Gavin, the Ralph Bunche senior fellow for Africa policy studies at the Council on Foreign Relations. “They believe that to counter US interest is somehow by definition in South African interest.”

South Africa’s main opposition and business leaders have warned that the Lady R row could disrupt commercial ties to the US that are critical to the country’s blackout-plagued economy. South Africa exported more than $15bn worth of goods to the US in 2021 under the African Growth and Opportunity Act, a US law that grants duty-free terms to specific nations.