Three men and a teenage boy have been rescued from rough seas in Torres Strait, after their boat capsized and left them stranded on a channel marker overnight.

The group was winched to safety by a rescue helicopter on Monday morning, more than 16 hours after they set off from Seisia Wharf on Cape York.

Police said they had been travelling home to Moa Island on Sunday when their five-metre boat capsized while refuelling about 5:30pm.

The group was reported missing later that night, sparking an overnight search involving a fixed-wing aircraft and a vessel.

It's believed the vessel flipped over during the refuelling process. ( Supplied: Queensland Police Service )

Water police found the men, aged 51, 38 and 21, along with a 16-year-old boy, about 900 metres from their boat in North West Reef, about seven nautical miles from Thursday Island.

Police said the group had been able to walk across the reef to a large channel marker during low tide and spend the night there.

A helicopter was called in to perform the rescue because of rough conditions.

All four were taken to Thursday Island Hospital for assessment.