Government spokesperson Phumla Williams on Wednesday said the report was submitted on Tuesday by the directors general who headed the investigation.
Ministers in the justice, crime prevention and security cluster would hold a news briefing soon to announce the outcome of the probe.
"Government appreciates the seriousness of this matter and appeals to the public to exercise patience."
Williams said the cluster was committed to ensuring that the outcome of the investigation resulted in "stringent measures being put in place to avoid a reoccurrence of such incidents in the future".
On April 29, a plane chartered by the Gupta family, carrying 270 wedding guests, landed at Waterkloof.
Guests were attending the wedding of Vega Gupta (23) and Indian-born Aakash Jahajgarhia at Sun City. The landing sparked widespread criticism.
Gupta debate
Last week, the ANC welcomed a debate on the use of the Waterkloof Air Force Base by the Gupta family.
"As an open and transparent forum for debate on matters of national importance, Parliament has a responsibility to reflect on this matter in the interest of the people of South Africa," said Moloto Mothapo, spokesperson for ANC chief whip Mathole Motshekga on May 9.
He said the ANC had proposed that the debate be scheduled from June 4 to 7.
Government said on May 3 that the landing at the national key point was unauthorised and that a probe was underway into a possible breach of diplomatic protocol.
Justice Minister Jeff Radebe said at the time that five high-ranking officials and military personnel had been suspended over the unauthorised landing.
On May 4, nine Tshwane metro police officers were arrested for allegedly escorting and providing unofficial security to Gupta wedding guests, from Waterkloof to Sun City. – Sapa