As the defence forces rally to help thousands stricken by the quake it may be up to a year before they can get back into their own Wellington headquarters.
Staff who work at Freyberg House and Freyberg Building in Aitken St were earlier told on Facebook the building would remain closed for the rest of the week.
A Defence Force spokesman confirmed Freyberg House had been damaged.
"The full extent of the damage will not be known for several days, and until that assessment is complete we cannot determine what work will have to be done or when it will be possible to reoccupy the building.
"We are considering a range of options for interim solutions, including remote working and relocation of staff to other NZDF facilities.
"The safety of our staff and those who work with us in other capacities is of paramount importance and this will remain our primary concern in the coming weeks."
RNZ is reporting engineers assessing the defence force headquarters have told staff it could be up to a year before they can return.
Earlier Chief of Defence Lieutenant General Tim Keating posted pictures of the widespread damage inside Defence House.
Keating tweeted: "We are working hard to get our HQ up & running, whilst ensuring the priority remains helping the people of Kaikoura."
It is understood there are splits in an important structural support beam damaged in this week's earthquake.
The security guard was critically injured and remains in hospital after surgery overnight.