More than 600 square nautical miles was covered in the search on Saturday after 41-year-old fisherman Colin Palmer's 45-year-old companion was found by a commercial fishing vessel in Townsville's Cleveland Bay about 6.30am.
The men were standing at the back of their boat when a wave knocked it, causing them to fall overboard about midnight on Friday.
The current dragged their boat away quicker than they could swim after it.
The pair attempted to swim back to shore but lost contact with each other during the night.
Aircraft will continue searching overnight with boats to re-join the search at first light on Sunday morning.
The 45-year-old man rescued on Saturday morning was taken to shore where he was treated for exposure.
He was taken to hospital in a stable condition.
Three helicopters and nine boats searched a wide area on Saturday, with agencies including Maritime Safety Queensland, Australian Maritime Safety Authority, Coast Guard, Volunteer Marine Rescue, Surf Lifesaving Queensland and QGAir involved.
It is unknown where the men fell into the water or where Mr Palmer may have ended up.
"We unfortunately don't have a starting point or reference point in relation to where the boat was," Queensland Police acting senior sergeant Jayson Cooke said.
"The gentleman (rescued on Saturday morning) was in the ocean for up to six hours, so it is a blanket search of the area at the moment."
Anyone who spots the four-metre, white Quintrex coast runner Queensland registration RD806Q is urged to contact police.
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