One shopkeeper who worked nearby said the town was in shock.
He said there had been a strong police presence in the town of about 800 earlier in the day looking for the boy. "Everyone is pretty sad about it. Pretty distraught.
"It's bloody shocking."
He said locals had not been told much other than that the boy had been with his dad on a boat.
People walking near the wharf at 8.30am noticed a large number of police cars and were told by some fisherman to keep an eye out for a 6-year-old-boy, another resident said.
A resident told the Herald he understood the boy went missing between 1am and 6am.
The boy's dad had checked on him at 1am and he was still sleeping, but when he checked again after 6am he had gone.
"They couldn't find him."
A check of the marina's security cameras showed that he had not walked onto the wharf.
The family did not appear to be locals.
Police said next of kin have been advised and the matter referred to the Coroner.
A post-mortem examination has also been requested.
It comes less than two weeks after 9-year-old Emily Branje was swept away and died while whitebaiting with extended family at the Hokitika River mouth on September 27.
Her body was found days later near the mouth of the Grey River near Cobden on the West Coast.
