South Africa's defence ministry has launched a probe into Iran's participation in the BRICS+ naval exercises held near Cape Town this week, after reports that President Cyril Ramaphosa had asked Iran to withdraw to avoid antagonising the United States.

There has been confusion over the past week over Iran's role in the drills, which also included Russia and China. A Reuters witness saw three Iranian ships in the False Bay area every day with the other vessels, but the defence ministry has not clarified what they were doing.

South African news outlets Daily Maverick and News24 reported that Ramaphosa had ordered Iran to be withdrawn from the exercises due to concerns about the damage its participation could do to South Africa's shaky relationship with Washington.

The inquiry will seek to determine whether Ramaphosa's instructions were misrepresented and/or ignored, the defence ministry said in a statement on Friday.

Defence Minister Angie Motshekga told Reuters it was untrue that the defence force had defied presidential orders, without giving further details. Ramaphosa's office has declined to comment.

The exercises came at a particularly sensitive time as US lawmakers were considering whether to extend the African Growth and Opportunity Act, a preferential trade programme for some African countries. The US House of Representatives passed the bill on Monday, though there is still a possibility that South Africa could be excluded.

The US Embassy in South Africa posted on social media on Thursday that it had noted with "concern and alarm" the reports about Iran's participation in the exercises.

US President Donald Trump has been threatening to intervene in Iran if a deadly crackdown on mass protests, which appear to be abating, continues.

BRICS+ is an expansion of a geopolitical bloc originally comprising Brazil, Russia, India, China and South Africa - and seen by members as a counterweight to US and Western economic dominance - that now includes several other countries including Iran, Egypt and the United Arab Emirates.

The exercises were described by South Africa as an operation to "ensure the safety of shipping and maritime economic activities".