He was elected to the council between the time the written submission was lodged and the hearings began.
Mr Wilson said guidelines from the Office of the Auditor General were "pretty clear from what I've read" that councillors should not vote on issues they had made pubic submissions on.
In an email to Mr Belford yesterday, Mr Wilson said: "You made a conscious decision to represent Transparent Hawke's Bay at the board of inquiry while you were a councillor regardless of submitting before the election."
He said Mr Belford was "clearly conflicted" when it came to any council discussion regarding the Ruataniwha scheme, so "at the very least" he should register his interest in the organisation.
"You will also need to consider [your] future involvement with decisions around RWSS [the Ruataniwha Water Storage Scheme]."
Asked about yesterday's email from Mr Wilson, Mr Belford said he had "nothing to add".
Transparent Hawke's Bay co-founder and chair Pauline Elliott said Mr Belford had been operating at "arm's length" from the organisation since being elected to the council and did not have a conflict of interest. "Fenton Wilson's call is an unsavoury and unnecessary challenge to Councillor Belford's integrity," she said.
Councillors are scheduled to vote late next month on whether to invest up to $80 million of ratepayers' money into the Ruataniwha scheme, a $275 million project designed to provide irrigation across about 25,000ha of land in Central Hawke's Bay.
All nine councillors have indicated they need further information on the project before making up their minds on how they will vote.
This month the council is due to receive a peer review from consultants Deloitte on the business case for the project, put forward by its commercial arm, Hawke's Bay Regional Investment Company Ltd.
The council will also carry out public consultation on the proposal this month.
The removal of Mr Belford's vote could be significant in deciding the fate of the project if councillors are split on the issue next month.
If he does not vote, the scheme could be approved or scuttled by four councillors rather than a majority of five or more. In the event of a 4-4 tie, Mr Wilson has a casting vote as chairman.