The female junior sailor who has accused a naval officer of spanking her repeatedly broke down in tears and yelled "It happened!" during cross-examination.

Lieutenant Commander John Alan Jones has pleaded not guilty to 23 charges relating to nine alleged incidents of indecency between February 1 and October 20 last year.

Five of those incidents allegedly involve him smacking the sailor's bottom.

The defence counsel's cross-examination of the sailor, who cannot be named, had to be halted several times during the court martial on Thursday when she broke down in tears.

She repeatedly shouted "It happened!" during counsel Lieutenant Commander Alister Abadee's questioning.

The sailor was giving evidence via video link to a court martial in Canberra as required by ACT law in cases involving allegations of sexual misconduct.

Lieutenant Commander Abadee questioned the sailor about inconsistencies between evidence she gave on Wednesday and the first witness statement she made in November 2010.

"Now as time goes on, I can remember more and more and more clearly," the sailor told the court martial.

She agreed with the defence counsel's suggestion she had relied emotionally on Jones, especially after her grandmother died in August 2010.

But several times, when Lieutenant Commander Abadee suggested she had allowed Jones to smack her because she thought he could use his power and rank to help her, she told the court martial she had never thought of it that way.

"He made me believe that I could trust him; he was like a father to me," she said.

Defence counsel asked the sailor whether seven of the nine alleged incidents actually did occur. Each time she insisted they did.

Lieutenant Commander Abadee suggested the sailor had consented to or allowed the other two alleged incidents to happen.

'Scared'

The sailor repeated her evidence from Wednesday, that she had been scared of Jones.

She said she did not tell anybody about the allegations because she was embarrassed and ashamed, adding that she still had nightmares about what she says Jones did to her.

"These things pounce up in my head... it's like a picture in my head," she told the court martial.

"I nearly took my life because of these things."

Earlier on Thursday the court martial heard a secret recording the sailor made in November 2010 of a conversation between her and Jones.

In the recording the court martial heard the sailor telling Jones she was stressed about the alleged smacking.

He told her it was for her own benefit.

"It wasn't so much that I wanted you naked, it was more a test to see how obedient and compliant you were going to be," he told her.

"Try and put it out of your mind and move forward."

The hearing continues on Friday.

AAP