Correctional Services spokesman Manelisi Wolela has denied allegations that student leader Mcebo Dla.
"The President regards all the investigations and reports into the upgrades as important," his spokesman Mac Maharaj said in a statement.
"He has responded to the National Assembly taking all the reports into account,"
On Friday, Public Protector Thuli Madonsela's office said Zuma had not yet responded to her report on the R246 million security upgrades.
"The document that is being disseminated does not respond to the Public Protector's report and, in fact, in the document it says this is not a comment on the Public Protector's report," spokeswoman Kgalalelo Masibi said in an e-mail to Sapa at the time.
"That means a document that comments on the Public Protector's report or indicates action taken or to be taken to implement remedial action in compliance with section 3(5) of the Executive Members Ethics Act must still be submitted to Parliament by the president."
However, Maharaj said Zuma was taking all reports into account.
"The Presidency has noted statements attributed to the office of the public protector stating that President Jacob Zuma had not responded to the public protector's report on the Nkandla security upgrades."
He said Zuma's response to the National Assembly took the joint standing committee on intelligence (JSCI) report, the public protector's report titled "Secure in Comfort", and the Special Investigating Units report into account.
Zuma submitted a response on the upgrades to his private home to Speaker of Parliament, Baleka Mbete, on Thursday.
In the response, Zuma requested ministers in the security cluster and the public works minister, Thulas Nxesi, to report to Parliament on their "clearly defined roles and responsibilities" when dealing with the president, the deputy president and their predecessors' security when implementing Cabinet policy.
He said Nxesi should urgently report to Cabinet on the review of protocols and procedures regarding procurement, expenditure and oversight applicable.
Lastly, Zuma said Cabinet should review the 2003 policy on the security of the president, deputy president and their predecessors with a view to setting parameters for implementation.
Earlier this year, Madonsela found that Zuma and his family had unduly benefited from the R236 million upgrades and recommended that he pay back some of the money.
Zuma declined to respond to Madonsela's report in full within the required fortnight and said instead he would wait for the Special Investigating Unit's findings on the upgrades.