A Taranaki District Health Board spokeswoman said a 31-year-old woman had been taken to Taranaki Base Hospital where she was in a stable condition in the Emergency Department.
Police said it was not clear why the boat sank.
There are conflicting reports from witnesses about when the couple crossed the bar yesterday. Some believe they saw the boat head to sea as early as 1pm. Others say it was later after sunset.
It is understood the boat safely crossed the bar but foundered in deep water.
The sunken boat is now being towed back to Port Taranaki.
It is unclear what kind of boat it was.
A local community board member and experienced boatie suspects the survivor may have been in the water for much of the night.
Clifton community board member Ken Bedford was perplexed by the sinking, saying conditions north of the bar were idyllic this morning with waves barely raising a ripple on the shore.
"It's as flat as a millpond. It must have happened either very, very late at night or early this morning around high tide," said Bedford.
High tide at Waitara was around 2am.
Up to 50 vessels had been successfully crossing the bar through the channel every day, he said.
It was highly unlikely the craft would have been taking the risk of getting over the bar at low tide.
