Police said last night that they were contacted by other members of their five-strong group just after midnight.
The three other men remained on the island, a police spokeswoman said.
She said the men had been on a boat launched from Whangaparaoa.
The alarm was raised after a diver did not resurface, and a second diver who went to investigate also disappeared.
The police Eagle and Westpac Rescue helicopters searched for the pair without success overnight Saturday before an aerial search resumed yesterday.
Their bodies were returned to Auckland for post-mortem examinations to be carried out.
Meanwhile, a Great Barrier local, who declined to be named, said he had heard the group were scouting for crayfish.
The men had been diving at night at Cecilia Sudden Bay - an area which left little room for error due to the narrow and fast moving Colville channel that runs between the island and Coromandel Peninsula.
Auckland Freediving spokesman Regan Hall said while the group may have had adequate lighting to see what they were doing, he had "never come across it before".
"I probably wouldn't do it myself."
Freedive NZ president Phil Clayton said people who chose to freedive at night would be well equipped with lighting and should be well aware of the risks, but diving in poor visibility and deep currents "increases the risk".