Police also began making inquiries with potential owners of the boat and a vehicle found nearby, Koefoed said.
A Facebook appeal for information was also made by police - a post that was spotted by the men who had been on the boat.
They called police to say they were safe.
"They reported the boat had become submerged and they had swum ashore on nearby Pepin Island.
"From there they rang acquaintances to help them get home."
The men had got a lot of the rules of boating safety right, Koefoed said.
"They were carrying their phones in a dry bag and they were wearing lifejackets, which is fantastic."
But police wanted to remind boaties to tell police immediately if they got into trouble.
"We take every report such as this incredibly seriously and if we had been contacted by the men earlier we wouldn't have had to launch a full scale search and take resources away from other areas.
"We're here to help, so any time you're in trouble, please call 111 right away."