A junior Navy officer who alleges she was sexually violated by a superior says she didn't report it because she didn't trust the military police.

Scott Christopher Devonport Ward is on trial at the Auckland District Court on a charge sexual violation by way of an unlawful sexual connection with a junior naval officer in October 2011.

The woman was under cross examination on Tuesday, the second day of the trial.

Defence lawyer Anthony Rogers questioned why she did not report the incident to a number of outlets available to her, including the military police.

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"I don't trust the military police," she told the court.

The woman said she knew as soon as she reported it, it would have been taken out of her hands and she would have been "dragged" to the naval and civilian police while her career "stood still".

"All throughout losing my career, my friends, everything."

Rogers also asked her why she didn't tell anyone the day after the incident when she had "the whole day" before the ship she was posted on left Wellington for Auckland following a weekend celebrations for the Navy's 70th anniversary.

"I was busy doing chart-work and I was scared to report what happened."

The woman said she also knew the defendant had been drinking at the Chief of Navy's house the night of the incident, which was another reason why she felt uncomfortable raising it.

Prior to the night of the alleged sexual assault, the woman said she'd only had strict and professional interactions with Ward.

"Anyone with gold on their shoulders was almost scary to me."

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The trial centres on allegations Ward entered into the woman's cabin and forced himself into her bed and sexually violated her.

The woman said yesterday the offending was "really painful" and "very violent".

"I kept trying to pull away and I tried to elbow him with my left elbow but ... I was pinned. I said stop, I said no. And he said, 'Shh just let it happen'. He just kept going and going."

She said she saw Ward again at a party in 2012 where he apologised to her two or three times but she said she just wanted to put it behind her and pretend nothing had happened.

However, after speaking to counsellors in 2014, the woman realised it still affected her and needed to deal with it so reported the violation to the police.

The trial continues tomorrow.