Waitemata councillor Mike Lee said the rule is likely to mean extra costs for people and create a parallel regulatory framework based on race.
Employers and Manufacturers chief executive Kim Campbell shares Mr Lee's view that it could lead to an unacceptable dual resource consent process.
"As it stands, the proposed Unitary Plan's cultural impact assessments would add uncertainty, cost and time delays to the issuing of resource consents," Mr Campbell said.
Albany councillor Wayne Walker said councillors were not made aware of the fish hooks when they approved the Unitary Plan for public notification last September.
In addition to the 3600 listed sites, he said there were large areas that could require assessments across outstanding natural landscapes, significant ecological areas and coastal areas.
"There are potentially big costs involved for property owners, Auckland Transport and Watercare because the land area covered is substantial and likely to grow as iwi add to it," Mr Walker said.
Council Unitary Plan manager John Duguid said homeowners must seek local iwi approval for works such as home alterations of more than 25sq m or the installation of swimming pools.
Activities such as gardening are exempt.
There are affected areas scattered across Auckland, including large swathes of Devonport and pockets of North Shore beaches.
Mr Duguid said the rule was not in the early draft of the Unitary Plan, but came about as a result of feedback from mana whenua groups.
David Taipari, chairman of the council's Independent Maori Statutory Board, said the rule was no different from those protecting built heritage, saying it was important that people did not destroy or affect archeological or sites of significance to mana whenua.
Councillors today will debate the council's submission on the Unitary Plan. By yesterday, 2370 submissions had been received on the plan.
Submissions close tomorrow.
Impact assessments
* 3600 sites in Auckland Council area of value to mana whenua.
* Homeowners and businesses will need an assessment from iwi to do work on these sites.
* If iwi do not agree, applicants must apply to the council for resource consent.
* Standard process being developed.