Mr Mooney believed the long and expensive flights to Wellington were due to the engine problems impacting the national carrier.
But Air New Zealand said demand had softened for flights and changes were made in December.
The reduction of flights has led to Mr Mooney having to travel a longer route, both in time and distance to make Parliament.
His new journey starts on a Monday afternoon, from Queenstown to Wellington, connecting in Christchurch.
When he returns on Thursday, he has to fly up to Auckland and then back down to Queenstown on a direct flight.
Mr Mooney was unsure about how much extra time he clocked up, but knew it was an impact on his time in Southland.
"I couldn’t tell you off the top of my head.
"[It just] means I have a reduced amount of time I can be in the electorate," he said.
"I hesitate to sound like I’m only worried about myself, but I am hearing it’s affecting a lot of people in a lot of ways.
"I know it’s not easy on Air New Zealand, they have their challenges, but this is having a real impact on people’s abilities to get around," he said.
He said the impact was not just on Queenstown, but the nation as a whole.
Mr Mooney believed the troubles surrounding the flights were due to the engines in the smaller planes used for regional and internal travel in New Zealand.
Mr Mooney said the restrictive travel around the country was an issue, impacting on multiple fronts.
"People need connection to family, connection to their medical appointments, for business.
"I heard, anecdotally, some people resigned their directorship positions because of it."
He said Queenstown was a really important hub.
"We’re not [isolated] to the eastern seaboard of Australia, in fact the flights between there and Queenstown are up 140%.
"We’re getting better and better connectivity to the Western Island, but less to the Northern Island you might say.
"To be honest, sometimes it is faster and cheaper to go to Australia than it is to go to Wellington [laughs].
"I laugh, but it’s actually true."
Mr Mooney said he was hoping for better investment by Air New Zealand into the Queenstown Airport, or for anyone who could to put their hand up.
Queenstown Business Chamber of Commerce chief executive Sharon Fifield said, in a statement, the reduced flights were having an effect, but there was positive momentum.
"Yes it is affecting businesses and we are communicating directly with Air New Zealand on this." she said.
"They are working hard to secure jet engines to reinstate the schedule as quickly as they can,"
Air New Zealand domestic general manager Kate O’Brien said the company operated two daily flights between Queenstown and Wellington, with no changes resulting from recent schedule adjustments.
It did not refer to engine issues impacting on the flight schedules.
"Those looking for alternative routes from Wellington to Queenstown can also connect via Auckland or Christchurch," she said.
"In December, we adjusted our services in response to softened demand, predominantly from corporate and government customers."
She said that included the Christchurch-Queenstown route, where the first flight of the day from Queenstown at 9am is now operated by an ATR aircraft and the final service from Christchurch to Queenstown departs mid-afternoon.
