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However, Mr Eggers said Nasa was ''moving forward'' with plans for infrastructure projects at the airport, including a new payload processing facility.
Warbirds Over Wanaka Airshow general manager Ed Taylor said the cancellation was disappointing.
Nasa brought ''quite a bit of economic stimulus'' to Wanaka, he said.
''When those Nasa guys are in town, there's a large number of them here and they are all staying locally and doing stuff locally, so it's good for the community.''
Mr Taylor said the airshow had a ''great relationship'' with the Nasa team in 2016 when it was ready to launch immediately after the show.
''They worked around us and started their first fly-day several days after the airshow so we could get all our major infrastructure packed down.
''They're good people to work in with and they brought something different for Wanaka.''
He expected the political situation in the United States would be sorted out in time for Nasa to return to Wanaka next year.
Mr Eggers said like previous launches from Wanaka in 2015, 2016, and 2017, the 2020 flight would be mainly designed to ''validate and certify'' the balloon technology.
The aim was to achieve long-duration flights, upwards of 100 days, at stable ''float altitudes'' of about 33km.
Nasa cancelled last year's flight, preferring to launch from Sweden.
The 35-day government shutdown from December 22 was the longest in US history and resulted from political disagreement over President Trump's call for funding to extend the wall on the Mexican border.