Air NZ last month announced it would suspend its Dunedin to Sydney service from April 16 to October 24, a move that has upset the university.
"It is disappointing the flights to Sydney were suspended," University of Otago chief operating officer John Patrick said.
The university had a preferred supplier agreement with Air NZ but would consider flying with a different airline if it offered a transtasman service from the city, he said.
"We meet . . . Air NZ on a regular basis and will be signalling our disappointment and adding our weight to others also wishing to see the flights reinstated," Mr Patrick said.
A direct Dunedin-Sydney flight gave the university more options than flying out of Auckland because "it is more time and cost-efficient for staff to travel direct from Dunedin".
The university was represented on the Project Gateway Committee, which has a goal of daily flights between Dunedin and Australia.
Its representatives are also expected to meet the airline to discuss the issue.
Air NZ and the university declined to say how much the preferred supplier agreement was worth, but it is understood the university is one of the airline's biggest corporate customers.
Tourism Dunedin chief executive Hamish Saxton said the university was a major customer for Air NZ, flying not just in New Zealand and Australia but "all over the world".
"It makes good business sense for the university to want to fly direct and connect with other international flights, and I am sure Air NZ will be listening to their concerns," Mr Saxton said.
Dunedin International Airport chief executive John McCall confirmed the airline had been in contact with the airport last week, but it was unclear whether any discussion would lead to the reinstatement of the twice-a-week service to Sydney.
"We are not surprised by what the university is saying.
"There are other businesses in the marketplace who feel similarly," he said.
The airport continued to "have discussion" with other airlines, notably Jetstar and Pacific Blue, about the transtasman route, "because we want to grow our business".
"In the past, it was said that the New Zealand domestic market could not support two carriers.
"It now supports three," Mr McCall said.
Air NZ had increased its domestic passenger numbers since the arrival of Pacific Blue last year and "there is no reason this couldn't happen with transtasman flights".
Dunedin people were taking advantage of cheaper flights from Christchurch, he said.
