Dunedin Police duty Senior Sergeant Trevor Thomson said it appeared someone tried to gain access through a door to the building early yesterday morning, and then smashed several exterior windows with a pipe.
"They have caused quite a bit of damage."
Anyone with information about the incident was urged to contact police, he said.
Pool manager Robyn Duggie said she was devastated by the "senseless" act, which has caused the closure of the facility for several days while the pool is drained and the glass removed.
Regular users of the pool, including those undergoing rehabilitation, "would suffer" as a result of the damage, she said.
"People are upset that some person has done this and caused a lot of unnecessary worry."
The pool was operated by the Otago Therapeutic Pool Trust, which spent between $20,000 and $30,000 a year to maintain it. The complex attracts more than 50,000 visits each year.