The Democratic Alliance was in possession of the letter, which it said was included in Parliament’s Announcements, Tablings and Committees (ATC) document.
In the letter, Zuma wrote there were “stark differences” in the findings and the remedial action proposed by the Public Protector’s report and that of the interministerial task team.
“This is clear from the reports as well as very public pronouncements made by the respective parties,” he wrote.
“In my experience in government I have not encountered such an anomaly.”
The DA said the response seemed to be attempting to “cook up” a narrative about the validity of Public Protector Thuli Madonsela’s report.
The opposition party accused Zuma of using the Special Investigating Unit (SIU) as a “king-maker finding” to break an invented deadlock between the two reports on the security upgrades to his private home in Nkandla, KwaZulu-Natal.
Parliament confirmed on Wednesday it had received comments from Zuma on Madonsela’s report into the upgrades.
In a statement on Wednesday, announcing Madonsela’s deadline had been met, the presidency said Zuma had noted in his response that three state agencies or institutions the Public Protector, the justice, crime prevention and security cluster of Cabinet, and the SIU had all probed the Nkandla upgrades.
Zuma said he would give full and proper consideration to all the matters before him and, upon receipt of the SIU report, provide Parliament with a further report on the decisive executive interventions he considered appropriate.
SIU spokesman Boy Ndala told Sapa on Wednesday that his unit’s investigation was still ongoing and would be completed at the end of next month. He said the status of the report shown on the SIU’s website as “completed” was not correct.
On Wednesday evening, the SIU changed the status on the report to “ongoing”.
Last month, Madonsela found Zuma and his family unduly benefited from security upgrades to his homestead and recommended that he pay back a percentage of the non-security upgrades.
The DA said on Thursday it was seeking legal opinion on whether it could force Zuma to abide by the Public Protector’s recommendations.
“The DA will not let the president undermine the Office of the Public Protector, or escape accountability,” the party said.
“He owes South Africa a full explanation and Parliament must now use its powers to ensure that this happens.”