He said the man could have swum to Reids Farm about 1km downstream and got out of the river there. He appealed to members of the public for any information that might help searches or establish the man's identity or location.
"We still haven't heard from anyone who knows the person."
Police received credible information from other swimmers at the hot pool who witnessed his disappearance about 200m downstream.
"However, if this person has swum successfully from Spa Park to Reids Farm, police are pleading for him to call."
The natural hot pool at Spa Park is where the Otumuheke Stream flows into the Waikato River, and is a popular attraction.
About 20 people were at the pools when the man disappeared.
Mr Shepherd said tonight the police would now reassess what further action might be required.