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The concern was raised at yesterday's planning and regulatory committee meeting, as councillors signed off on the council's submission on the Government's Building (Earthquake-prone Buildings) Amendment Bill 2013.
The Bill would give councils five years to assess nearly 200,000 buildings, including all non-residential and high-rise, multi-unit apartment buildings, for earthquake risks.
Owners of earthquake-prone buildings would then get another 15 years to upgrade to at least 34% of building code requirements, at an expected cost of about $1.7 billion.
The council's submission supported the Bill's intent, but argued against many of the changes, which council heritage policy planner Dr Glen Hazelton warned could cost the council $5.6 million in assessment costs.
Cr Kate Wilson told yesterday's meeting she was also nervous the changes ''may well'' impede progress in upgrading the city's heritage buildings under existing council policies.
She wanted that progress underscored in the council's submission, and found support from Cr Jinty MacTavish, who said the city's heritage buildings were an important part of the city's economic development strategy.
Any loss of momentum would come at a cost to the city, which should be stressed to the Government, she said.
''If we lose the momentum, for whatever reason, then that's a real opportunity cost,'' she said.
The council already had an earthquake-prone building policy, introduced in 2011, which gave building owners until July 1 next year to provide the council with initial assessments at their own cost.
However, the council's submission warned some building owners were already scrapping plans to pay for their own assessments, in anticipation of a change in Government policy.
Cr Lee Vandervis told the meeting the Government's ''knee-jerk reaction'' against heritage buildings also ignored the fact the majority of fatalities from the Canterbury earthquakes occurred when more modern buildings collapsed.
''I believe the whole Government reaction to the terrible events in the Christchurch earthquake has been to minimise some council and government responsibility for very bad buildings built not that long ago, and to push it on to heritage buildings,'' he said.
Committee chairman Cr David Benson-Pope said the submission would be fortified to underscore that.
Dunedin Mayor Dave Cull said the entire lower South Island was overrepresented when it came to older buildings and the likely economic impact of the proposed changes, but Dunedin was ''the extreme example of that''.
Dr Hazelton said the council wanted a regional approach to new rules, as well as the ability to prioritise some areas, such as George St, and types of improvements, such as parapets, over others, he said.