The official's email said: "If he were to complete his posting prior to 30 May and return to Malaysia with his family, that would be the end of the matter."
Rizalman returned to Malaysia on May 22, against the wishes of the Government, police and the victim of his assault.
Yesterday he was sentenced to nine months' home detention after pleading guilty to indecently assaulting Wellington woman Tania Billingsley in her home in May 2014.
The report's author John Whitehead said he accepted the MFat official's assurance that she had not intended to suggest that the New Zealand Government was seeking anything other than a waiver of immunity.
"However, on the basis of a straightforward reading, the email does not clearly explain that 'the matter' relates only to the court fixture and not the incident as a whole, as the protocol officer stated was her intention.
"I consider, therefore, that inadvertently the email provided scope for the Malaysian authorities to misunderstand the intent, as subsequently proved to be the case."
The issue was made worse by the fact that the email was not distributed to other ministry staff, so they were unaware of the official's comments.
Attached to the official's email was a formal note, which included the ministry's official position that it wanted immunity to be waived.
Mr Whitehead said MFat's mishandling of the case had had serious effects, especially for the victim.
"The woman who had suffered traumatically from the alleged incident was left for a considerable period of time with the impression that she would not see justice done in New Zealand," the report said.
Ministers were "seriously embarrassed" and "angry" at the turn of events, staff in the minister's office and at MFat had their reputations put at risk, and the ministry's positive reputation was damaged.
New Zealand's diplomatic relationship with Malaysia could also have been jeopardised, the report said, "if it had not been for mutual efforts over a number of years to build a strong and positive relationship".
"None of this was intended, of course, but it followed from the initial misunderstanding of the intent behind the email."
Green Party women's affairs spokeswoman Jan Logie said the report highlighted the failure of Government ministers to show leadership on sexual violence.
"Ministers were told about the attack on Ms Billingsley well before Muhammad Rizalman bin Ismail was allowed to leave the country," she said.
"The Minister of Foreign Affairs and police both had an opportunity to show leadership and to ensure that officials treated the attack seriously. Instead they removed themselves from the review.
"By excluding themselves from the investigation, they further perpetuated their lack of political leadership on this issue."
Victim advocate Louise Nicholas reads statement on behalf of Ms Billingsley:
The protocol officer who sent the email resigned from MFat last year, but has picked up another Government job.
In his report, Mr Whitehead said there was "definite evidence" that the protocol officer "clearly regarded the incident itself as a very serious matter".
He said the staff member had a history of "zero tolerance for even minor misdemeanours by foreign diplomats, let alone for crimes at the more serious end".
At the time of the incident, Prime Minister John Key criticised the MFat official.
"If that person doesn't have clarity about that position then they need to think very strongly about whether they're in the right job," he said.
Foreign Affairs Minister Murray McCully said the findings of the investigation were "disappointing".
"As previously indicated the conclusions reached by Mr Whitehead's investigation are not unexpected but they are very disappointing," Mr McCully said.
"At the heart of the matter is a single email, along with procedural shortcomings, which gave Malaysian officials the impression it would be acceptable for Mr Rizalman to return to Malaysia."
Mr McCully said that Rizalman had now been through the court system, but this process should never have been in doubt.
"I would also like to reiterate my apology to the young woman who was so badly let down by the way this issue was handled."
At a press conference today, Foreign Affairs Minister Murray McCully said he took responsibility for the shortcomings at his ministry.
He said the report "paints a picture of serious failure on a serious matter" and the ministry's reputation had been damaged.
Mr McCully said that although the terms of reference for the review did not include scrutiny of ministers, he was interviewed by Mr Whitehead and his emails were made available to the inquiry.
Asked whether it was plausible that he did not see a crucial email sent to his office until weeks later, he said: "All I can say is that I was extremely disappointed about that.
"I think the best thing I can do is accept the findings in the report. Some might say they were generous in that respect.
"I would simply say I respect the work that Mr Whitehead's done."
Asked whether any disciplinary action would be taken as a result of the damning findings, he said the report was not designed "for employment purposes".
The protocol officer at fault is no longer at MFAT, and then-chief executive John Allen has moved on to another government role.
Mr Allen offered his resignation to Mr McCully at the time of the incident, but it was not accepted.
The minister reiterated his apology to Ms Billingsley, saying she had been let down.
The Rizalman saga
May 9, 2014: Muhammad Rizalman bin Ismail, a military attache at the Malaysian High Commission, alleged to have attacked Wellington woman Tania Billingsley in her home. He is arrested.
May 10: Rizalman charged with burglary and assault with intent to rape. New Zealand asks Malaysia to waive diplomatic immunity.
May 22: Rizalman leaves New Zealand with immunity after a mix-up between New Zealand and Malaysian officials.
June 29-30: The case is made public. An inquiry begins over how the diplomat was allowed to leave.
July 2: Malaysia confirms Rizalman will be returned to New Zealand after psychiatric assessments.
October 22: Foreign Minister Murray McCully confirms a court case concerning Rizalman's extradition has taken place in Malaysia.
October 24: Rizalman returns to New Zealand and appears in court.
December: A report into MFat's handling of the matter by ex-public servant John Whitehead is completed but not released.
November 30, 2015: Rizalman pleads guilty to indecent assault.
December 15: Judge decides Rizalman had a sexual motive when he entered Ms Billingsley's house.
February 4, 2016: Rizalman sentenced to nine months' home detention.
February 5: Whitehead report released.
