Among those missing was the British Olympic yachtsman Glyn Charles, who was swept off the Sword of Orion when the boat rolled in the heavy seas. The two sailors who died were from the yacht Business Post Naiad, one suffering a heart attack and the other drowning. The other seven crew members were winched to safety.
Despite the horrendous conditions, with winds gusting up to 70 knots and waves reaching 25ft, organisers said the 630 nautical mile race was unlikely to be called off.
Until now there has only been one death in the race known as "Hell on High Water".
As night fell, a full-scale search, involving 30 civil and military aircraft, was under way for the missing crews, which included two women. One of the missing yachts was the veteran cutter, Winston Churchill, which was built in 1944 for the inaugural race.
A total of 37 out of 115 yachts have been forced to retire from the race; in most cases the yacht has lost its mast or a crew member has been injured.
Brian Hill, of the Australian Maritime Safety Authority, which was co- ordinating the search, said the conditions were very hard.
"The problem is that when yachts are dismasted they often lose their communications."
The storms are the worst since 1993 when huge seas and 75-knot winds hit the fleet, sinking two boats and forcing 66 out of the 105 yachts to retire.