The Southern Clams managing director said the three-stage project was "very expensive" but was the only way to demonstrate the effect on the community.
The company began harvesting cockles from the middle banks of the harbour in September after the Ministry of Fisheries approved a research permit.
Most of the harvest is going to the United States and Asia.
The research was in response to concerns raised by local runanga and members of the public as to the effect of commercial harvesting, he said.
"We are absolutely convinced that our style of harvesting is sustainable. We wouldn't be doing it if it wasn't," Mr Belton said.
He believed his business was a good use of resources which allowed for "optimum stocking" of cockles.
"The impact will be very similar to what we have experienced and demonstrated over the past 25 years in Blueskin Bay and Papanui Inlet, but we are prepared to invest in this research to put public concerns to rest."
Ryder Consulting senior environmental scientist Dr Brian Stewart was contracted to carry out the work, which started yesterday.
He and three others spent the day taking the first of 280 core samples from harvested and controlled areas on the harbour's middle banks and were scheduled to finish today.
These samples will be analysed in a laboratory looking at flora and fauna, and the composition of sediment in the substrate.
This would take about two weeks.
"Our job is to determine if the harvesting is having any impact on the communities," Dr Stewart said.
If the research showed the fauna, with the exception of the cockles, had no significant differences compared with those in the control areas, commercial harvesting would continue into phase two when a larger survey would be undertaken in the summer of 2011-12.
If significant differences were apparent, the first exercise would be repeated in 40 days.
The Ministry of Fisheries will review each phase; it must be satisfied no adverse effects to other species were caused before allowing the next phase to begin.
At the completion of the project, Southern Clams has no assurance of right being given to commercially harvest.
Otakou runanga project manager Hoani Langsbury said "we are keeping a close eye on what's going on with the research".
He was concerned about the sustainability of commercial cockle-harvesting and the effect it could have on all marine animals in the area.
He also questioned if five years of analysis was adequate, believing an extended period of time might have different effects.
If a mataitai, driven by Otakou runanga, is approved, all commercial fishing will be banned in the harbour.
