In an interview with Radio New Zealand, the corporation said the tourism industry is firmly in support of keeping the flights.
They said the government needs to work with the people of Aitutaki to come to a solution.
“We call upon the community in Aitutaki and we call upon the government to engage with the stakeholders in Aitutaki so that this issue can be solved, so that it can be sorted, for the benefit of the community and the benefit of the industry.”
However, tourism refused to answer questions from CI News on whether or not the referendum would be further impacted by the announcement of Jetstar flights from Auckland to Rarotonga on Tuesdays, Saturdays and Sundays.
In a referendum in April, a majority of the island's population voted to end Sunday flights to and from Rarotonga, with those wanting the ban saying Sunday is a sacred day when businesses shouldn't operate.
Prime Minister Henry Puna, called the referendum as part of a campaign promise in the lead-up to a by-election on the island, but has still not said whether he will honour the result.
He last answered questions on the issue back in August, admitting at a press conference that he was “fearful” of making the wrong decision.
The PM said that was why he wanted to be very careful in how he handled the controversial issue.
“I believe there is a way forward, and that by engaging in ongoing dialogue with our people, the way will become clear.”
He said the need for balance on issues involving conflicts between religion and commercial activities meant that everyone involved needed to take time to really consider the issues, and work out a way forward that was “appealing and agreeable” to everybody.
Meanwhile, director of destination development Metua Vaiimene has welcomed the announcement that Jetstar will start flying to Rarotonga in March in a deal which will mean an extra 25,000 return seats to the country every year.
The flights will originate from Sydney or Melbourne, and Australian travellers will connect to Rarotonga via Auckland.
Vaiimene says tourists from New Zealand and Australia are the country's biggest markets, and the new flights will provide more choice and competition.
"It is our largest industry. It's the biggest provider of employment and income here in the Cook Islands.
“So it's important to continue to invest in that and diversifying the ways in which our visitors can come here, like approaching new airlines such as Jetstar, as part of our overall strategy."