The change would also increase the tourism potential between Wellington and Victoria, he said.
It was "well-timed for business-related travel and of course gives Wellingtonians more travel choice to an Australian city that's widely liked here".
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Calling it a shame to lose the direct connectivity with Canberra, Fry said nevertheless a strong awareness of Wellington as a tourism destination had been developed in the Australian capital.
But Jordan Williams of the Taxpayers' Union took a dimmer view of the change, calling the route's subsidies "corporate welfare at its worst" and saying it should be scrapped.
"The Wellington-Canberra route should never have been subsidised in the first place," he said.
"Now that the spending has proven to be a complete waste, you would expect WREDA to scrap it.
"Instead, the agency says they'll subsidise the new route – despite there already being regular flights between Wellington and Melbourne."