The woman had hoped to get to Dunedin and the man was only going to Arrowtown. However, he decided to change his plans to help the young woman.
But she told police she asked the man to drop her at Cromwell after he allegedly made advances.
Police said they have received several reports from witnesses who saw the woman hitchhiking and also after she was dropped off at the Cromwell public toilets, behind the Z Petrol Station.
A bus driver had come forward saying that he saw a young woman in a "distressed state".
She eventually caught "public transport" to Dunedin.
A Queenstown photographer told the Herald she recalled seeing the woman standing on the side of the road in the rain at 8.55am and feeling sorry for her.
"It was absolutely pouring with rain and she looked freezing cold and was shivering. She looked like she wasn't really dressed to be standing in the rain hitchhiking. She didn't look very happy, she looked very cold and I hoped that someone would pick her up quickly."
The witness said a man was standing about 5m in front of the woman, also hitchhiking, but he looked more prepared for the conditions wearing a big, hooded jacket.
She said she had phoned police and told them what she had seen but was yet to hear back.
The hitchhiker didn't look like a tourist, rather someone who had visited the town for the weekend.
"I thought she looked like [she] got a little caught out, I mean who knows really, but she just had a little weekend bag."
"She didn't have the clothing on that suited standing out in the rain hitchhiking. I think it was a denim jacket or something but i remember thinking it didn't look like a very warm jacket."
The woman said she would have picked the hitchhiker but she was travelling in the opposite direction.
Police this afternoon urged hitchikers to be careful.
"Members of the public can be assured they are at no immediate risk but police would like to reinforce that people hitchhiking need to take great care before accepting lifts," police said in a statement.
"Hitchhiking or accepting rides from people you don't know is not recommended. If you do decide to hitchhike, police strongly advise you not to travel alone.
"Make sure there is always someone who knows where you are going and when you should arrive at your destination."
They said an option for hitchhikers was to use the SAFE programme run by Spark which allowed people to record the vehicle they get into, the time of travel and travel route.