The Auckland Council has found two high-rise buildings clad with combustible panels similar to those implicated in London's Grenfell Tower disaster.
The council has not said which buildings are affected, but says they are privately-owned and the material is being replaced with fire-proof cladding.
Aluminium composite panels with a polyethylene (PE) core are suspected to be behind the rapid spread of last week's fatal apartment block fire in London, and another 600 buildings in England are being urgently tested.
Of New Zealand's three biggest cities, only Auckland has investigated to see if buildings there use similar cladding.
Last week it said it had detected no inappropriate use. But it said yesterday it had now found two buildings over 25m high with PE panels.
Neither Wellington nor Christchurch had done any investigation into the panels until being asked to begin this week by government officials.
Despite this, Building and Construction Minister Nick Smith last week told Morning Report his officials were "reasonably confident" the combustible panels "have not been used in high-rise structures" in New Zealand.
Dr Smith said he was advised last year that "we had no evidence it was being used" but decided to get ahead of the curve and order restrictions.
Auckland Council was continuing to check 88 other buildings, but was having trouble determining what type of aluminium composite panels (ACP) they had. The database it used could not search by cladding type.
The council did not reveal which two buildings were affected, what they were used for, or if owners or renters had been told about the cladding.
The buildings, which both have sprinklers, were in the process of being "remediated with a fire-rated cladding system", the council said.
Checks not started until this week in Wellington, Christchurch
Auckland Council began checking its buildings after a briefing in February last year about the 2014 Docklands fire in Australia, which identified 10 big ACP high-rise cladding fires since 2007.
The council said when it realised fire regulations allowed the combustible ACP on buildings up to 25m tall, it petitioned the ministry to tighten the rules.
Announced in January, the restrictions kicked in just three weeks ago to limit the use of the panels to buildings under 7m high, which would be one or two storeys.
Dr Smith said last Friday it was "a fair question as to whether there were any multi-storey structures built with this cladding type prior to the regulation change".
"The advice I had at the time was they thought it was unlikely because these products had not got a hold or been significantly used in high-rise structures prior to us making the regulation," he said.
He had asked the Ministry of Business, Innovation and Employment (MBIE) to contact major city councils and ordered "further checks to be done".
The following Tuesday, a letter from the ministry asked some councils including Christchurch City and Wellington City to investigate.
It said the ministry was "keen to understand if there are systemic issues from the use of ACPs".
"I am asking for your help to allow MBIE to build a picture of how ACPs are used across New Zealand," it said.
Christchurch City Council said until this week it "had not been formally requested to investigate any inappropriate use of ACPs".
"We have only now begun this investigation. The council does not keep data regarding the number of high-rise residential buildings that have used aluminium composite panels."
Any audit, it said, "would take some time".
Wellington City Council similarly had not been asked prior to this week to do any checks.
"At the direction of MBIE in the past week, we have started a process aimed at identifying if materials of a similar nature are present on local buildings," it said. "This survey, of many thousands of building consents, could take weeks or months."
As the combustible panels look no different from the fire-rated ones, and consent paperwork could be unreliable, any inspection might have to take a sample and test it to be certain.