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The plan requires a change of zoning for the affected land.
Cr Dave Cull this week said "plan change 7" contained "ghastly negative repercussions" that would lead to hundreds of job losses.
He has sided with the Otago Chamber of Commerce and five businesses which have appealed to the Environment Court against the change.
Cr Cull said he did not know how many other councillors also opposed the plan change, but believed the matter needed to be debated by the council in public and the plan modified.
At this week's planning and environment committee meeting, an attempt by Crs Cull and Kate Wilson to introduce a notice of motion over the harbourside plan was turned down by committee chairman Michael Guest.
The Otago Daily Times has obtained a copy of the notice of motion Crs Cull and Wilson attempted to submit to the planning and environment committee meeting.
It calls on the committee to recommend to the council that stage two of the proposed plan change (which has the greatest effect on existing businesses) be withdrawn and that staff report on ways to "remove or minimise the risk of reverse sensitivity".
Cr Guest told the Otago Daily Times a notice of motion should go to the full council. The next council meeting is on March 29.
Cr Cull would not detail the motion he wanted to put but believed the council's plans for the harbourside were flawed. His main concern was about the future viability of the businesses in the affected area.
"They figure that reverse sensitivity issues will force them out, force them to close and there will be hundreds of jobs lost."
It would be seen as reverse sensitivity if, for example, the residents of new apartments complained about noise from existing industrial activities in the area.
The harbourside district plan change was approved in February last year after a nine-day public hearing in 2008.
The change means land zoned industrial and port will be zoned "harbourside".
The plan was described by chief executive Jim Harland as "a 50-year vision".
In April, the chamber and five companies lodged appeals with the Environment Court against the plan change.
Cr Colin Weatherall then led a council delegation to meet the appellants in a bid to reach an agreement that would avoid a costly court battle.
Chamber of Commerce chief executive John Christie said the chamber was in negotiation with Cr Weatherall but "this issue is one that we believe even he doesn't think can be solved by the court process".
Mr Christie said that, at Cr Weatherall's suggestion, the chamber approached Mayor Peter Chin for "an audience".
"We think council are aware of some of the issues but unfortunately there are many, many more issues that we have discovered in the process of investigating this on behalf of the businesses we're representing."
The chamber's approach was rejected and Mr Chin told the ODT it was not appropriate for the council to discuss the plan change with the chamber while it was progressing through the judicial system.
"The matter is being dealt with by Cr Weatherall and everybody is aware of that process."
Mr Christie said the chamber was not against harbourside redevelopment and improved public access.
"We're against this particular plan change [which] we believe will be detrimental to the future of industry to be able to exist there as it does currently. It will ultimately cost the city a substantial number of jobs."
Cr Cull said the plan change would create a "huge risk" to businesses through the issue of reverse sensitivity.
"If you zone it so people can actually live next to a foundry, it shouldn't be much surprise to anyone that it might give a few problems in the long run, with the residential neighbours complaining about the noise and smell."
Cr Cull said two industries employing 200 people "could be forced to close".
It could also deter offshore oil-exploration companies from using Dunedin as a base.
He believed some aspects of the plan, around the harbour basin, were acceptable but other aspects needed to be modified.