Corruption Watch has called on President Jacob Zuma to remove Deputy Defence Minister Kebby Maphatsoe, following his claim that Public Protector Thuli Madonsela works for the CIA.

Maphatsoe's claim amounted to contempt of the public protector in terms of the Public Protector Act, chairman Archbishop Njongonkulu Ndungane wrote in a letter to Zuma on Wednesday.

"The statements, which are not supported by a shred of evidence, imply that the public protector is guilty of treason and are so serious that they fall to be interpreted as hate speech and the incitement of violence against the public protector," he wrote in the letter.

"We view these remarks as an attempt to intimidate all those intent upon combating maladministration and corruption."

Earlier this month, it was reported that Maphatsoe, also the Umkhonto we Sizwe Military Veterans' Association chairman, had accused Madonsela of being a spy, insinuating she worked for the US Central Intelligence Agency.

Madonsela gave Maphatsoe three days to back his allegations, or issue an apology and retraction. The following day he apologised, but claimed he had been misinterpreted.

"After consultation with my organisation, the African National Congress, it would seem as though my statements have been misunderstood and misinterpreted," he said at the time.

"I therefore withdraw those statements and apologise for any offences and hurt that would have been caused."

Ndungane called Maphatsoe's apology "conditional".

"In light of the deputy minister's conditional apology and the lack of evidence to support his spurious claims, it is apparent that the statements were made only to denigrate the public protector and her office and reveal a complete disregard for the integrity of the office," he wrote in his letter to Zuma.

"The law provides for powerful sanctions that may be imposed for conduct that holds the public protector in contempt and these must be enforced in this case."

Corruption Watch on Wednesday wrote to Madonsela urging her to pursue contempt charges against Maphatsoe.

"We in civil society cannot countenance the weakening of the public protector and will do all in our power to defend the institution," Ndungane wrote.

"We therefore urge you to vigorously pursue contempt charges against Mr Maphatsoe and to seek the most stringent penalty provided for in the law."

Madonsela said she was evaluating Maphatsoe's apology.