"The SIU wishes to announce that it handed its final report to the presidency late yesterday afternoon, that is, 20 August 2014," spokesman Boy Ndala said in a statement.
Zuma submitted a response on the R246 million upgrades to his private Nkandla homestead in KwaZulu-Natal to National Assembly Speaker Baleka Mbete last week Thursday.
The presidency said he had taken all reports into account.
There were three different investigations into the upgrades, done by the joint standing committee on intelligence, the public protector, and the SIU.
Earlier this year, Public Protector Thuli Madonsela found Zuma and his family had unduly benefited from the upgrades and recommended that he repay 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 SIU's findings.
Public spending on security upgrades at his Nkandla homestead have turned into one of the major controversies of the Zuma presidency, as costs escalated to R246 million. It emerged the project included a pool (dubbed a "firepool" by government), an amphitheatre, a cattle kraal, and a chicken run, among others.
On Friday, Madonsela's office said the response handed to Mbete by Zuma did not respond to Madonsela's report.
The presidency and the African National Congress's chief whip Stone Sizani disagreed with Madonsela's statement saying Zuma had responded.
The National Assembly on Tuesday resolved to set up an ad hoc committee to consider Zuma's response.