Lead archaeologist James Robinson of Heritage NZ said as well as the shell tool fragments the earlier dig uncovered a moa pelvis, a one-piece fishhook of the type made by early Maori, and fragments of clay tobacco pipes.
The pipes were in the French style, so could be linked to du Fresne, who visited Moturua several times.
After his death his crew attacked Paeroa Pa on the other side of the island, killing many of its inhabitants.
The problem with the previous finds was that their context and age were unclear. Mr Robinson said there was a "moral imperative" to finish the job.
On Wednesday a team of volunteers located the trench dug in 1981, using old photos and probes to feel where soil had been disturbed, and re-excavate it.
They also excavated a nearby stream bank.
If the team found any artefacts similar to those from the previous dig their exact location would be recorded and dates ascertained.
"We know the site is early. The question is, how early?" he added.
New finds on Wednesday included a possible moa bone spear tip, a kuri (dog) tooth and a piece of red ochre shaped into a crayon-like form.
Ochre was used to decorate everything from bones to paddles.
If the fishing lures were found to be pearl shell, and dating confirmed the site was as early as suspected, that could mean it was used by the first generation of Maori and was as old as Marlborough's Wairau Bar, the most famous of the early sites found so far.
And if the pipes were shown to be French they would be a "very exciting" link to du Fresne, Mr Robinson said.
"In the best case we have a very early site with a famous French explorer at the top. Even in the worst case, if the pipes are not French, it is a continuous site from the first arrival of Maori to the earliest European explorers. It tells us part of the early story of the Bay of Islands, and gives an insight into what people did when they first arrived here."
Ngati Kuta and Patukeha were closely involved. Kaumatua Matu Clendon said he had a special connection to the island, having been born and raised there.
Hapu members were helping with the dig, keeping the site secure overnight and ensuring tikanga was followed.
The archaeologists' findings added another dimension to the basket of knowledge, he said.
"We don't need to dig to know our korero is our korero," added Kipa Munro, an iwi advisor to DOC. "But if this allows our stories to come to life, that's great. Every layer we go down just verifies the korero we tell our children and grandchildren," he said.
DOC archaeologist Andrew Blanshard was instrumental in getting the project started.
Last year he managed to obtain the 1981 notes and bagged materials from Auckland University, contacted Heritage New Zealand, and enlisted the support of Ngati Kuta and Patukeha.
The University of Otago, which had two Master's students and a research assistant on-site, will carry out the analysis and carbon dating, the most expensive part of an archaeological study.
Costs will be covered by a Marsden Fund grant.
