In response, the Malaysian High Commission said it would not waive immunity and had "decided that [Muhammed Rizalman] should be repatriated to Malaysia as soon as possible".
It also asked MFAT and New Zealand police to "kindly consider sealing all documentations pertaining to the above mentioned matter and [withdraw] all charges against Mr Muhammed Rizalman Bin Ismail".
The High Commission said it would ensure Muhammed Rizalman did not return to New Zealand in the future.
The documents conflict with comments made this afternoon by Malaysian Foreign Minister Anifah Aman, who said Malaysia was willing to drop immunity but decided to invoke it after an offer by New Zealand officials.
Officials 'acted in good faith'
Foreign Affairs Minister Murray McCully said tonight he had spoken with his Malaysian counterpart to clarify any misunderstanding around the diplomatic standoff and issued a press statement to say the Malaysian authorities acted in good faith.
Mr McCully said the miscommunication seemed to have occurred during "informal communications over what is a complex case, in a manner that would have been ambiguous to the Malaysian Government".
Any evidence gathered by the New Zealand police would be placed before the military Board of Inquiry, said Mr McCully.
"The Minister made it clear that he would not allow the actions of one individual to tarnish the reputations of all Malaysian diplomats," said Mr McCully.
"It is clear to me from my conversation with Minister Anifah that his Government's decision to decline New Zealand's request for immunity to be lifted was driven by his Chief of Defence's desire to put in place a robust judicial process to deal with this matter and his officials' belief that this would be an outcome acceptable to New Zealand."
'Stern action' to be taken
Malaysian Foreign Minister Anifah Aman told reporters in Malaysia this afternoon that a defence ministry panel will investigate the junior official and "stern action will be taken" if he is found guilty.
He said the accused will be sent back to New Zealand "if it is absolutely necessary".
Asked to elaborate, Mr Anifah said he will be extradited if New Zealand requests it or if New Zealand thinks the Malaysian investigation is not being conducted properly.
Muhammed Rizalman returned to Malaysia on May 22.
Mr Anifah said it was never Malaysia's "intention to treat the matter lightly".
He said Muhammed Rizalman was sent for medical check-up after his return.
"His physical state is satisfactory. However, he is now under psychiatric evaluation to assess his mental and emotional condition."
The defence ministry had established a board of inquiry to investigate the case and had given an assurance that "it will not compromise or conceal any facts on the case being fully aware that Malaysia's good name is at stake", Mr Anifah was quoted as saying.
The Malaysian Government took the issue seriously.
"The Malaysian Government acknowledges that the incident is a serious matter and we do not have any intention to sweep the matter under the carpet," Mr Anifah said, according to AP.
Fight to name diplomat successful
An urgent hearing to overturn the suppression ruling was held in the High Court at Wellington today, where the name suppression was overturned.
Media organisations, including the New Zealand Herald, challenged the decision to grant name suppression.
Foreign Affairs Minister Murray McCully earlier said the Solicitor-General had advised the Government abide by the suppression ruling while it was in place.
"I can't see any good public policy reason why you'd want to protect someone from publicity given there won't be a trial."
Muhammed Rizalman, in his 30s, left the country after being charged by Wellington police with burglary and assault with intent to rape.
He had followed a 21-year-old woman to her Brooklyn home on May 9 when the alleged assault occurred.
MFAT called in Malaysia's Head of Mission last night to tell them that New Zealand expected Muhammed Rizalman to face the consequences of his actions.
Prime Minister John Key said the country had reassured MFAT that they were taking the issue very seriously.
"We made it quite clear that we were under no illusion about how seriously New Zealand took the issue, and we expect the person to be held to account," he said.
Lawyer for the media organisations, Robert Stewart, told the court the appeal related to a decision by Judge Bruce Davidson to grant name suppression.
His notes had not been released into reasons why he granted name suppression, which left media "flying blind" because they would not know which aspects of the decision to appeal, he said.
The Malaysian Government was issuing a statement at 4pm today (NZT), where at least the country, and possibly the man's name would be released.
Media here would then be in a situation where the rest of the world would have the details, but if they shared those details, they would be in the "extremely invidious position" of breaching court orders, Mr Stewart said.
Muhammed Rizalman was not represented at court, but Barbara Hunt acted as the court's amicus in the matter.
Police lawyer Grant Burston said the Crown's position was they did not oppose the appeal.
There did not seem to be an evidentiary reason for the judge to order name suppression as it would not identify the victim or prejudice any future trial because the man had invoked diplomatic immunity.
Justice Collins had the file in front of him, but there were some hand-written notes of Judge Davidson's he was unable to read.
Ms Hunt was the man's lawyer on the day of his first appearance and applied for the initial name suppression.
That was because he had not yet told his family, but he was represented by his employer.
Also because of the seriousness of the charge and health issues that needed to be explored, she said.
In later court dates the man had not been represented, she said.
"His interests do need to be considered."
Read the NZ Government's letter to Malaysia here:
Read the response from Malaysia here:
- Additional reporting NZ Herald