It is estimated that up to 25,000 buildings will need strengthening work, but this number could dramatically increase. Only a third of councils have good records on the health of their building stock, and the number of buildings needing strengthening could jump to 40,000.
"A bit of this is flying blind," Mr Williamson said.
Data published in the Government's consultation paper showed around 400 buildings in Auckland would collapse in a moderate earthquake.
However, this was only a fraction of the complete picture.
The data also showed that 4300 buildings - with unreinforced masonry - were being assessed by the council. Many more buildings could be found to be below the safety threshold and would therefore need to be upgraded or demolished.
Property Council chief executive Connal Townsend said that while Wellington had a huge head-start in its assessment and remedial work, Auckland was lagging behind.
"I think Aucklanders are almost completely oblivious to the issue. And I think in this city people are just beginning to wake up to ... the massive size of it.
"I'm quite amazed that Aucklanders utterly believe that earthquakes can't occur here. My personal view is that Aucklanders are living in a fools' paradise."
At public meetings last week, property owners expressed concern that New Zealand did not have the experts needed to perform the huge number of assessments required within the proposed five-year timeframe.
Institution of Professional Engineers New Zealand chief Andrew Cleland confirmed there were probably not enough structural engineers to complete the job.
He said: "The Christchurch City Council put a requirement out for assessment on buildings with a relatively short timeframe and it simply didn't work because there were not enough skilled people around to do it."
Mr Cleland said that migrant engineers would need to be brought in and trained in order to meet the demand for seismic assessments.
Mr Williamson said that if the experts could not be found the Government would concede that the proposed five-year window would have to be widened.
Auckland Council has asked for a 15-year timeframe for strengthening buildings, but not because of any concern about the availability of experts.
It felt that a 10-year deadline would amount to an "execution order" for the city's heritage buildings.
The minister said exemptions or more lenient timeframes could be considered for Category 1 heritage buildings.
"There are small towns in New Zealand where there are huge numbers of their buildings that are in the Historic Places category but will be very, very hard to justify the sums of money to bring them up to an earthquake-prone standard."
But he emphasised that Government wanted strong national guidelines and too many exemptions would create an ineffectual plan.
Property developer Ian Cassels owned Erskine College, a four-storey heritage building in Island Bay.
He said it would cost him around $10 million to upgrade it to the level the Government proposed, which was a third of the new building code.
But unlike the Auckland Council, he did not see the Government's proposals as an "execution order".
He believed a new assessment regime would prompt communities to consider what value they placed on their heritage, and what their priorities were.
There has been some resistance to the Government's proposals from property owners, who said negative seismic assessments would undermine the value of their buildings, making them worthless for up to a decade.
One Wellington property owner told officials: "On the day that the council sends its letter, the value is destroyed instantly. "
Mr Williamson had little sympathy. He said the public had a right to know which buildings were safe.
He envisaged a public register for the country which would allow New Zealanders to check on their smartphone if a cafe was safe before they bought a coffee there.
The minister stressed the importance of finding a balance of safety and cost in identifying and repairing New Zealand's ailing building stock.
The rate of assessing and improving earthquake-prone buildings in New Zealand was sluggish and needed to accelerate dramatically.
But making the timeframe for strengthening too short or the standards too strict would "bankrupt the country".