Meanwhile, a proposed $10 million revamp of the Wanaka museum is on hold indefinitely.
Mr Brodie (52) has worked at the museum since it was founded in 1992 by Sir Tim Wallis.
His wife, Diane, has worked as a museum administrator for the past four years.
The couple said they were sad to be leaving their home in Luggate, which had been a great place to raise their children and live, but they were excited about their new opportunities.
New Zealand Fighter Pilots Museum charitable trust chairman Don Spary said while it would be business as usual at the museum, Mr Brodie would be greatly missed.
"Ian has been an absolutely fabulous, loyal person... and goes with our best wishes," Mr Spary said.
The Brodies' jobs would be reviewed but the remaining staff, including administrator Mandy Kirner and weekend assistants Graham Taylor and Bob Holland, would continue to work for the trust, Mr Spary said.
"It is obvious in the present recession the major scheme we had earmarked will not be proceeding in the short term," Mr Spary said.
The museum development was proposed in 2001 and designs were commissioned in 2002.
The then prime minister, Helen Clark, launched a fundraising campaign in 2006, but the project has not progressed beyond plans.
"We just need to continue to operate until circumstances change to where we could look for a major fundraising and expansion," Mr Spary said.
The New Zealand Fighter Pilots Museum attracts between 20,000 and 25,000 visitors a year, up from 8000 in 1992.
Mr Brodie said he was looking forward to his new position and was great friends with Russell Alexander, who owns the Matamata farm that film-maker Peter Jackson transformed into Hobbiton for the Lord of the Rings film trilogy.
The farm is now a successful tourist business.
A new set, for Jackson's film of The Hobbit, is being created at the original Hobbiton site.
Mr Brodie is the author of the top-selling Lord of the Rings Location Guide Book and many other books on airshow and film topics.
In his new role, Mr Brodie will help develop the Hobbiton and farm tourist attraction, which has had about 170,000 visitors since it opened and employs about 15 staff.
His tasks will include advertising, website design, media liaison and promotions.
The avid Tolkien fan would also be able to add "authenticity" to tourists' Lord of the Rings experience.
Mr Brodie will continue his other roles as an international airshow commentator, including at Warbirds Over Wanaka 2010.
He will continue to write books and work as a speaker for tour groups and at conferences.
Mr Brodie said Lord of the Rings products were still having an impact on visitor numbers, several years after the Oscar hype had died down.
The Matamata i-site figures revealed 54,000 visitors in 2001, leaping to 242,824 the following year when LOTR fever struck.
The figures reached 367,000 in 2003 and have stuck around 300,000 ever since, Mr Brodie said.
"So it keeps on going. Which is why I am going," Mr Brodie said.
