The defence lawyer for a top navy officer facing a court martial for not disclosing an affair says military investigators failed to collect vital evidence.
Commodore Kevin Keat has pleaded not guilty to eight charges of breaching the Armed Forces Discipline Act. The woman has name suppression.
Military prosecutors say Commodore Keat didn't disclose the relationship when questioned and told the woman to lie about it on her security clearance forms.
But defence lawyer Michael Bott told the hearing at Trentham Military Camp in Upper Hutt on Wednesday that there were problems with the investigation from the beginning.
Mr Bott says investigators only managed to retrieve one month of text data between the pair because they did not act quickly enough.
He says they made no attempt to independently confirm parts of the woman's evidence and took her complaint at face value.
On Monday, the woman said she tried to end the relationship during a phone call at the end of 2011, but Commodore Keat threatened to end her daughter's military career.
In a video interview shown to the hearing on Wednesday morning, Commodore Keat said he had a brief fling with the woman but it ended in 2010 before he became her superior - not late last year as she claims.
Commodore Keat said he never threatened her daughter's job, and didn't tell the woman to lie on her security clearance.
Difference of opinion, says Defence chief
The Chief of the Defence Force told the hearing there was a dangerous difference of opinion between Commodore Keat and a colleague about whether they were in a relationship.
Lieutenant-General Rhys Jones gave evidence on Wednesday morning that the woman told him about the affair in October 2012.
But General Jones said Commodore Keat claimed the affair ended before he became the woman's superior. He says he told the commodore the pair needed to discuss their relationship status, and must not lie about it if it continued.
General Jones said he asked the Vice Chief of Defence Force at the time, Rear Admiral Jack Steer, to monitor the outcome. He said Admiral Steer did not reveal that he had already questioned Commodore Keat about the affair in 2010.