A search is underway for the missing woman.
It would be the second fatality involving a crocodile in a fortnight.
On May 17, Noel Ramage, 72, drowned after a crocodile reportedly overturned the boat he and his mate were in while crabbing near Gunn Point, about 40km northeast of Darwin.
The Victorian man was trapped under the capsized tinnie and drowned while his 72-year-old friend hurled spanners and spark plugs at the croc in a desperate bid to keep it at bay.
The friend was trapped in muddy mangroves for three hours before he was rescued.
David Ramage said a croc had overturned his father's boat, but crocodile expert Dr Adam Britton, a researcher at Charles Darwin University, told AAP he'd never heard of such a thing.
He said the croc may have been attracted by the men's crab pots and they could have panicked, causing the boat to capsize.
The case has echoes of a fatal croc attack near the Daintree River just before Christmas in 1985.
Beryl Wruck, 43, was taken by a 5m croc after a fateful decision to take a late-night dip in the shallows of Barratt Creek, which feeds into the Daintree River about an hour's drive from Thornton Beach.
Wruck and several other party-goers had been cooling off after an evening of dancing and drinking. Witnesses told of seeing a huge swirl in the water and of Wruck disappearing without a scream.
Five-year-old Jeremy Doble died when he was attacked by a 4.3m crocodile in a swamp behind his Daintree River home.
He vanished in February 2009, with his seven-year-old brother telling police he saw a croc in the water moments the boy disappeared.
- AAP
