Government and the African National Congress (ANC) have distanced themselves from Deputy Defence Minister Kebby Maphatsoe's claim that Public Protector Thuli Madonsela works for the [American] Central Intelligence Agency (CIA).

"We released a statement saying [what he said] is not a government position. He was speaking in his personal capacity," government spokesperson Phumla Williams said when asked whether Maphatsoe could face disciplinary action.

"We are not in a position to comment. It is a matter for the executive."

ANC spokesperson Zizi Kodwa said Maphatsoe was speaking as Umkhonto we Sizwe Military Veterans' Association (MKMVA) chairman.

"The matter should be taken to the MKMVA."

Kodwa was responding to a statement by the National Union of Metalworkers of SA that it was not good enough for the ANC to say on Monday that Maphatsoe's comments were "unfortunate".

"The ANC needs to investigate Maphatsoe's statement and take appropriate action. The organisation cannot just hypocritically wash its hands," spokesperson Castro Ngobese said.

In its earlier statement, government said Maphatsoe's comments did not represent its views.

"Government distances itself from such accusations as they were never discussed at any official government meeting, nor do they reflect the views and thinking of government," Minister in the Presidency Jeff Radebe said.

"Comments or allegations against any country or persons, including those responsible for guarding and upholding constitutional values, should be raised and addressed at appropriate platforms. South Africa enjoys a cordial diplomatic relationship with the United States of America."

Radebe, who is also the chairman of the inter-ministerial committee on information and publicity, said the government reiterated its trust in Chapter Nine institutions, like the public protector.

It was reported on Monday that Maphatsoe accused Madonsela of being a CIA agent.

"We can't allow people to hijack the ANC. We'll fight and defend the African National Congress. uThuliumele asitshele ukuthi ubani ihandler yakhe [Thuli must tell us who her handler is]," Maphatsoe reportedly said in Soweto on Saturday.

"They are even using our institution now.... These Chapter Nine institutions were created by the ANC but are now being used against us, and if you ask why it is the Central Intelligence Agency. Ama [the] Americans want their own CEO in South Africa and we must not allow that," Maphatsoe reportedly said.

However, at a press briefing later on Monday the MKMVA denied the statement, but conceded that a reference to the CIA had been made.

US Embassy spokesperson Jack Hillmeyer confirmed on Monday that the country's ambassador to South Africa, Patrick Gaspard, would lodge an official diplomatic complaint about the allegations.

Madonsela has given Maphatsoe three days to prove his claim.

"She also expects Mr Maphatsoe to issue a retraction and public apology within the said period, failing which she will be left with no choice but to invoke the contempt of the Public Protector powers in terms of sections nine and 11 of the Public Protector Act," her spokesperson Oupa Segalwe said.

According to the act, it is a crime to insult the public protector.

Christian Democratic Party leader Rev Theunis Botha said the ANC had to stop criticising Madonsela.

"In fact, many ministers and other office bearers can take a leaf from Madonsela's book as to how they should perform their duties with integrity," he said.

Madonsela has come under attack from the ANC and some alliance structures since sending President Jacob Zuma a letter last month. In it she cautions him not to second-guess the recommendations she made in her report on security upgrades to his Nkandla, KwaZulu-Natal, homestead.

The National Freedom Party Youth Movement said it was "extremely disappointed" by Maphatsoe's comments.

"We all know what used to happen to people who were called spies or accused of being one," it said.

"Kebby Maphatsoe's utterances that advocate Thuli Madonsela was the enemy of the ANC and government is inciting violence against her. We view this senseless and barbaric statement as a message that Adv Madonsela must be dealt with the same old ways they used to do."

During apartheid, alleged government collaborators or spies were "necklaced", which involved placing a tyre filled with petrol over a the victim's head, dousing it with petrol and setting it on fire.