The men are yet to be identified but are believed to be from the group of four who launched an ageing runabout from a beach at nearby Cremorne on Sunday morning.
On board were three Hobart men – aged 26, 32, and 33 – and a 35-year-old New Zealander, police say.
One of their girlfriends raised the alarm on Sunday afternoon when they failed to return on time.
Two aircraft and up to six boats searched a vast expanse of water based on drift patterns, marine police inspector Lee Renshaw said.
The operation, including a foot search of nearby beaches and cliffs, continues for the two other men.
Insp Renshaw had warned earlier in the day that if the boat had sunk, the chances of survival were slim in water temperatures as low as 10C.
“Survivability in that temperature of water isn’t good,” he said.
Weather conditions including winds of up to 15 knots overnight are not expected to have caused difficulty for the boat, which Insp Renshaw described as old and had only recently been purchased.
“The men, who left on their fishing trip in a 16-foot (4.9 metre) fibreglass vessel about 7am yesterday, were believed to have access to life jackets but were not carrying an EPIRB,” the officer said.
He could not comment on the boating experience of those on board.
Records last picked up a signal from two of the mens’ mobile phones about 9am on Sunday.
Police will prepare a report for the coroner.
“Our thoughts are with the families involved,” Insp Renshaw said.
A Toyota Kluger and empty boat trailer remain on the beach nearby where the vessel launched.
A marine wind warning is in place for southeast Tasmania which could hamper ongoing search efforts.
The Bureau of Meteorology expect the rough conditions to stretch through until midnight Tuesday.