Emergency services including a rescue helicopter were sent to the scene about 1.30pm on Wednesday, with police divers entering the water.

People on another boat helped pull one man out the water before alerting emergency services, police said.

Earlier, Queensland Ambulance Service said one man was flown to Princess Alexandra Hospital in a critical condition.

Police have since confirmed both men have died.

The men were fishing when the boat capsized in windy conditions near Green Island, between Manly and North Stradbroke Island.

Authorities are continuing to search the area, but police told reporters they believe only the two men were on board the vessel.

AAP