The Government is providing $2.1 million from its Waste Minimisation Fund for the project and stakeholders are contributing $1.7 million.
Waikare Oyster Waste Recovery (WOWR) was formed last September and organised a barge with a digger on it to extract the mud and shell build-up that had made the farms unsuitable for aquaculture. It started work in January, washing excavated shell in a huge tumbler on the barge, using 6000 litres of water hourly to flush silt back into the sea.
The shell was stockpiled at Opua for sale to cement or lime fertiliser manufacturers.
An initial one-month trial was extended to three months, with the barge stopping work on March 6 after clearing half of the farms.
Waikino peninsula engineer Andrew Lush initially supported the shell extraction, but is now preparing submissions criticising "woefully inadequate" Northland Regional Council monitoring and officials' failure to anticipate the mobile nature of the silt.
Northland Inc general manager Wayne Hutchinson said complaints of water being muddied had been investigated, but nothing could be attributed to the clean-up work.
It was the first time such a clean-up method had been tried anywhere and the process was being reviewed, he said.
Of the 24 closed oyster farms in the inlet, 12 had been restored to commercial standards and three of the remaining farms required the biggest clean-up of any of them.
Mr Hutchinson said WOWR had to look at ways it could do that job as the dredge/wash method might not work. "We've got to find another way to clean those three farms most affected by sediment," he said.