The building was purpose built for Statistics New Zealand in 2005 and the government department recently signed a 16 year lease on the building which is owned by CentrePort - a company owned by the Greater Wellington Regional Council and the Manawatu-Wanganui Regional Council.
It must now find temporary accommodation for its 500 staff.
MacPherson said like staff she had been left questioning why such a modern building had bit hit so hard.
"I am sure you are asking, and it goes without saying I am asking the same questions I am sure you asking - how is it a building as new as Stats House with the code rating that it had - could suffer this sort of damage?"
In a statement CentrePort chief executive Derek Nind said the company had been working on upgrades to the building based on advice from earthquake engineers before the quakes hit.
"We had just completed upgrades of the upper floors, which performed well.
"A small part of the ceiling on the ground floor and the first floor have partially dislodged after two concrete beams became separated from the exterior wall of the building."
Nind said two of its commercial buildings - the BNZ and Customs House - performed well and the company was working with tenants and engineers on a timetable for reoccupation.
But Statistics House and Shed 39 - where the Greater Wellington Regional Council was based - would require more extensive inspections to assess the level of damage.
"Engineers will conduct further assessments in due course.
"We understand this is challenging and confronting for customers and tenants and we've continued to keep them updated on the situation."
Nind said the port also suffered damage to some wharves and roadways with some liquefaction and differential settlement in places.
He said staff were working hard to get assessments done so the port could resume operations safely and as early as practicable.
A CentrePort spokesman said the building was fully compliant with the 2004 code when it was opened in 2005.
It was then re-assessed in 2013 after the Seddon earthquakes and found to be 90 per cent up to the current code.
"It was still an incredibly robust and well-designed building."
He said three of the floors had been upgraded recently and those floors had stood up well to the quakes.
It was the lower levels which had been damaged.
Asked why the relatively new building had not stood up to the latest shakes he said: "It is quite isolated damage. As was proven in the Canterbury Earthquakes mother nature will do what she will."
He said no one had been into the building since the quakes as Wellington was still getting plenty of aftershocks and it was not safe.
Earlier reports of the building pancaking were not correct, he said.
