Ms Fraser, who was intellectually impaired, disappeared from regional Victoria while heavily pregnant 13 years ago.

The 23-year-old discharged herself from a Bendigo hospital against medical advice on the night of June 20, 2009, before jumping on a train after telling people she wanted to go to a party in Cohuna.

But she never made it to the party.

Investigators and Ms Fraser's family believe she may have been murdered by her unborn baby's father.

Three men were named as possible fathers - Peter "PJ" Jenkinson, Gareth David and Tony Gatt - during an inquest into her disappearance that began on Monday.

Mr David was interviewed by police after Ms Fraser's disappearance.

At the time he told police there was a chance he was the father of her baby, which was due just days after she went missing, the Coroner's Court heard.

He said they had sex in a lane behind a Bendigo pub in August or September 2008, and if the baby was his it could cost him his marriage.

But Mr David walked back this story, while giving evidence by videolink to the inquest.

"When I look back now, I just don't think we had sex," he said on Monday.

"We might have kissed and cuddled."

He said he asked police to change his statement at the end of the 2009 police interview, but this was not recorded in the transcript.

"I wished to correct a few statements and the lady detective was writing it down," Mr David said.

But a lawyer representing Victoria Police said the post-interview conversation did not take place.

Ms Fraser discussed trying to talk to a man named Gareth in her diary and wrote "he denies me even being pregnant and told me never to call him again".

She also wrote about hearing from Gareth four days before she vanished and she "might be talking to him face to face tomorrow".

Mr David said he did not meet up with Ms Fraser and didn't find out she was pregnant until he was interviewed by police. He also denied being asked to take a DNA test.

Earlier, Ms Fraser's mother Karen told the inquest she believed her daughter may have been killed by her unborn child's father.

"Maybe she told someone they were the father and they didn't want to be and things got out of control and somebody accidentally hurt her," she said.

"I just can't imagine anybody hurting somebody so vulnerable."

She said Ms Fraser told her she did not know who the father was, but contemplated doing a DNA test since she had a few different partners.

Her father, Neil Fraser, said she attracted "undesirables" who had no work and used her to buy drugs or cigarettes since she received a disability pension.

Ms Fraser received a 40-second call from a public phone at 11.59pm on the night she disappeared.

Almost three hours later, her mobile phone was pinged by a tower in Leitchville, 27km from the town of Pyramid Hill where she was last seen.

More than 20 witnesses will give evidence over six days, as the inquest before coroner Katherine Lorenz continues.

Australian Associated Press