Chief of Army Major General Lou Gardiner said the theft was an attack on everything that soldiers had fought for in the last century.
"The value of these medals is what they symbolise and what they were awarded for. They were awarded for extraordinary valour, for courage and commitment and come to symbolise what our military forces have committed to over the years. It's a lot more than just monetary value.
"My message to the thieves is that you've stolen an important part of New Zealand's heritage. [These are] just not some medals for some medal collector. They symbolise some huge sacrifices that New Zealanders, over a century worth of conflicts, have actually put in for their country."
Defence Minister Phil Goff said the theft was a crime against the nation.
"These medals are national treasures. New Zealanders will be appalled and disgusted at the greed and self-interest of those who have stolen the medals."
The museum's executive trustee, Lt Gen (Rtd) Don McIver, said the medals would be worth millions on the black market.
"Some of them will be hard to sell. Every one of them is identified by name on the medal and in that context they could be identifiable as stolen.
"But that wouldn't mean hard collectors wouldn't be prepared to have the medals, even if they couldn't display them.
"They can't be replaced. You can get replicas of the medal sets, but they are known as replicas and in terms of value, it's nominal."
The family of New Zealand's most decorated soldier, Captain Charles Upham, last year sold his VC and Bar for an undisclosed amount, estimated to be well in excess of $1 million.
When asked to describe what he thought of the offenders, Mr McIver said: "I don't think I could out loud."
Inspector Steve Mastrovich said the thieves seemed to know what they were looking for.
"Entry was gained through a fire escape at the back of the building ... by smashing a window and opening a door.
"They targeted the Valour Alcove, which is where the gallantry medals are kept. It looks as though it was well-planned and well-executed.
"Some material was left behind, so it looks like they possibly had an idea of what they were looking for."
He said the thieves only broke into one display cabinet before escaping through a fire escape door. He had yet to determine how they fled the scene.
Major General Gardiner said there were no leads at this stage.
All security measures at the museum - including reinforced glass, security patrols and security cameras - had worked as they should have.
"In an event like this the security will be looked at again. But all the standard operating procedures were activated and ... everyone's done the right thing at the right time," he said.
Video footage has been handed to the police. Border control had also been put on alert in case someone tried to tae the medals out of the country.
The medals that were stolen belonged to the museum, families of war heroes and trusts. All artefacts in the museum are insured.
The museum director was last night making contact with all families of medal-winners.
Police have set up a hotline - 0800 349 0606 - for anyone that may have information leading to the recovery of the medals.
