Thomas was placed in a compartment directly behind her.
"Pretty much from the word go he began making sexual comments.
"He was saying things like calling me a filthy slut ... things similar to that effect. These sort of things carried on for the next 20 or 30 minutes," Ms Clark said.
She said when they got to about Featherston his tone changed and he became frustrated and angry.
"Right after that he said to me, after he gets out, he is going to hunt me down, get a car, and run me over and rape me."
She said when the comments began she turned and looked through a window separating the front, where she was seated, and his face was almost against the window of the prisoner compartment.
Ms Clark said she was "100 per cent sure" it was Thomas making the comments.
She said she did not answer Thomas at all or acknowledge what he had said. He then quietened down and there were no further comments.
Ms Clark said once they arrived at the prison she did not deal with Thomas, as she did not feel safe.
Defence lawyer Jock Blathwayt said Ms Clark did not know how many prisoners were in the back and did not know who was talking.
"You don't know that it was Thomas that was saying it. It could have been any of the three people [prisoners]," Mr Blathwayt said.
Thomas chose to speak in his defence and denied making the comments to Ms Clark.
When asked if that meant Ms Clark was lying he said "must be because I didn't say those words".
"There were two others in the back. The other two were yelling out things, I think," Thomas said.
Judge Bill Hastings said the evidence from both Ms Clark and Thomas was almost completely contradictory.
"On the evidence I have heard, I find Constable Clark's version of the events as credible and it's her evidence I prefer. For that reason, I find that the police have proved the charge beyond reasonable doubt," Judge Hastings said.
He said the offending was at the low end of the range of offending the charge encompassed.
"In view of that, I think a short term of imprisonment would be appropriate." Judge Hastings sentenced Thomas to three months' imprisonment.