The pair were taking part in a training exercise on Swan Island, south-east Australia, last week.
They used the vessel to reach Corsair Rock, a remote spot popular with surfers.
The officers have not been identified. No details have been given about the disciplinary measures.
The area off Point Nepean National Park is known for having some of the best waves in Victoria state. The place is hard to reach and surfers often travel by boat.
"We are aware of an incident where two Water Police members used a boat for personal use following a training exercise," Victoria police spokeswoman Natalie Webster was quoted by the Herald Sun as saying.
"The members have been spoken to in relation to the matter and disciplinary action has been completed."