The boat was removed in pieces on Tuesday and barged to nearby Whale Bay, then trucked to a yard for inspection by Maritime New Zealand, which is investigating the sinking.
Northland harbourmaster Jim Lyle said the last floating debris, including fish bins, had been collected on Wednesday.
All that remained was some heavy debris such as steel tanks and a winch on the seabed. They would be removed as soon as conditions were suitable.
Meanwhile, in Ruakaka, the first attempt at cutting up the P.Lee Can on Wednesday morning using a 20-ton digger and a truck failed but contractors, Lawson Cartage, returned to the beach that afternoon.
Company director Ann Lawson said her workers cut a hole in the yacht's hull using a concrete saw and retrieved its engine and gearbox.
"We cut up a lot of it at low tide [Wednesday] and early [yesterday] morning. I'd say most of it will be gone by the end of [yesterday]," she said.
Five workers were yesterday retrieving the yacht's stainless-steel rigging and timber.
She expected the entire salvage work to be completed by the end of this week.
The Northland Regional Council will pay the contractor an estimated $7000 before sending an invoice to yacht owner Geoff Phillips and his wife Ayla to reimburse the amount. The P.Lee Can, registered in Southport, Australia, ran aground on the beach about 11am on December 26.