Mr Spary announced in a media release the museum's future might be more secure if it was more closely aligned with the two-yearly Warbirds Over Wanaka airshow.
Planning has started to try to cement a new future with the Warbirds Over Wanaka Community Trust, which runs the airshow.
When contacted for clarification, Mr Spary said the museum has had a "tough time" since 2006, but he had not given up on the dream to redevelop the museum in some shape or form, so it could continue to be of regional significance and a significant tourist attraction.
"It is important to ensure in the next six months we continue to operate.
"We have had a tough time.
"There has been a whole lot of things.
"All the hopes we had that [former prime minister] Helen Clark would do something at the launch [of a $10 million redevelopment plan in 2006] fizzled.
"It was a killer.
"A lot of people who might have helped were at that launch.
"If the Government was not going to do anything about it, why would they?" Mr Spary said yesterday.
The community trust's chairman, Murray Cleverley, said it was mutually beneficial for both trusts to work together.
There was no doubt the museum was a valuable asset worth protecting for future generations, he said.
"We're conscious of the fact that the synergies between the two organisations, both from the event and the museum, are really close.
"One promotes the other.
"There are a lot of opportunities . . . to be strongly associated with the museum and it would enable us to have a dedicated presence for the 23 months between airshows," Mr Cleverley said.
The 16-year-old museum houses memorabilia, medals, weapons and aircraft from World War 1 and World War 2.
The personal stories of New Zealand's 95 fighter aces are also told in photographs, displays and audio-visual presentations.
When the trustees launched the $10 million redevelopment plans in 2006, the goals included moving to the former Alpine Fighter Collection's hangar and increasing visitors from 25,000 to 75,000.
The trust has struggled to find a major benefactor, has also faced increased competition for funding during the economic recession, and has suffered from a "significant drop" in visitor numbers, affecting cash flow, Mr Spary said.
The museum does not receive funding from the Queenstown Lakes District Council, but the council and the RNZAF Museum would be involved with the future planning.
Long-serving curator Ian Brodie recently left his position and now works at the Hobbiton tourist attraction at Matamata.
The museum remains open.
