"The biggest loser in the move will be Sabahans," he warned, Wednesday.
Fernandes who has plans to operate long haul AirAsia X flights out of Sabah besides launching new regional routes from the State said the problem he has is with the airport as moving to Terminal One would mean burdening his passengers.
"We don't want to do that because we have invested a lot of time in Sabah and we love the place.
But I cannot make money if airport tax is RM65.
No one is going to fly. You want us to use aerobridge, expensive terminals, the fare is going to go up and we'll kill the market," he said.
Fernandes said during its infancy when AirAsia was just starting out, Terminal Two charged the same airport tax as Terminal 1 and the traffic was small.
"But as soon as the airport tax was reduced in both Terminal Two of KKIA and LCCT in Kuala Lumpur, we grew so rapidly. Count how many international (AirAsia) flights there are in Kuching? One.
Because I'm paying RM65," he said, adding that KKIA Terminal Two has more international flights than Penang for AirAsia.
He added that when they opened the Miri-Singapore route with the airport tax set at RM65, the business deal turned out to be a disaster and the airline had to close the route. Once the tax was reduced to RM25, the flights are always full nowadays.
"It's very sensitive. It's not rubbish I'm talking about. RM20, RM30 makes a difference. And if I'm with the airport, and there's an airline which wants to invest RM3billion to develop new routes É it's the volume, don't forget every passenger who comes internationally may buy duty free or something else. It looks pretty clear to me."
According to him, AirAsia had brought in 30 million tourists to Sabah over five years and opened up new routes, including nine international ones such as Hangzhou, Shenzen and Jakarta as well as new domestic routes such as Penang and Kota Baru in Kelantan.
Fernandes said the airline is targeting to bring in 13 million tourists a year into Sabah over the next five years.
Fernandes who took over Philippines' Zest Airways earlier this week said his plan of making Kota Kinabalu the hub of the BIMP-EAGA is coming to fruition and once Air Asia X starts operations, Kota Kinabalu would be the Dubai of BIMP-EAGA.
"The only thing we need now to make my dream real is the airport.
We have been in constant discussion over this matter. For me, we don't care where we are as long as the cost is cheap.
"We don't want to go to Terminal One and our passengers have to pay RM65. Why should Sabahans pay more when we want to make it cheaper?
Right now, everything is expensive, what we have done is make travel affordable.
"We hope Malaysia Airports Berhad (MAB) and the State Government would consider to either expand Terminal Two or build a new terminal," he said, adding that he would be willing to develop Terminal Two himself if he was given the chance.
He said Air Asia X should have started its operations in Kota Kinabalu two years ago, bringing with it employment opportunities and extra tourist receipts, if not for the airport trouble.
"That is the next stage, bringing Air Asia X here. Sabah is going to help me justify the financial side of it in making it happen," he said, adding he has the full support of Chief Minister Datuk Seri Musa Aman on the matter.
He said he met Musa earlier in the day and was told about the 700-acre Tanjung Aru Development Plan.
"It makes sense to have a big terminal right by the development, " he said.
Three years ago, Fernandes pledged to fight tooth and nail against moving its operations to Terminal One, including chaining himself to the Terminal Two fence if necessary.
The proposal for AirAsia to operate from Terminal One was part of the Federal Government plan to convert Terminal Two into a cargo terminal, arguing that having all the carriers at Terminal One would streamline operations that would benefit air travellers especially those who need to switch flights.
However, critics favour budget carrier flights to stay put at Terminal Two because it would cause congestion if everything is concentrated at Terminal One. Besides, they said it did not make sense for Terminal Two - the main air entry into Sabah until 1985 - to be a cargo terminal after spending over RM1 billion of taxpayer's money to upgrade and expand it.