"Somebody could be working away in some dark corner to find a way to get into the systems of an ATC that we don't know about."
Airways was searching for the "best of the best" technology to counter this and bring back to New Zealand, Fulcher told the New Zealand Airline Pilots Association conference in Christchurch last week.
But the association says it is worried, especially about "virtual towers" where high definition pictures of what is happening around an airfield are transmitted to another location.
"Cyber-attacks cannot be prevented and therefore they introduce an additional risk into the ATC/ATM system. You can guard against their succeeding and also limit their success - none the less, they cannot be totally prevented. You need to ensure that both your systems and their related protections are both robust and up to date to mitigate this," said technical officer David Reynolds.
The banking sector spends billions attempting to prevent such attacks, however they still occur.
"Virtual towers and their communications/data links are very data rich, transmitting and receiving enormous amounts of data. Cybercrime for terrorist and political purposes is increasing and so does the threat," he said.
Virtual towers operated as a network rather than operating as a separate or independent control tower.
"A network is far more vulnerable. The cost of a virus entering the system or their being 'spoofed' - the aircraft or controller receiving corrupted information - is a major concern with a network of virtual towers."
Plane crashes with related loss of life could very possibly dwarf the cost of building a new tower, said Reynolds.
International Federation of Air Traffic Controllers president and chief executive Patrik Peters told the conference there was a shortage of about 2000 controllers in Europe and 40,000 around the world.
"I think there is a misconception that automation will meet that need. Automation will assist us to do our work but it will not take over," he said.
Peters, who is a manager at the Eurocontrol agency overseeing air space in Northern Europe, said there were cyber security risks with satellite-based systems that were coming.
''I'm sure they will manage somehow but at this moment in time we are still having these challenges to overcome."
Fulcher said Airways was studying where towers in areas of low traffic could be replaced by virtual towers as part of a transformation over the next decade and beyond.
"I don't think it's going to happen tomorrow but definitely in the next 10 to 15 years there will be more virtual towers around New Zealand because it just makes sense economically and from a safety point of view and from a contingency perspective."
He said it cost $50 million to $60 million to build new towers in some centres while virtual towers would cost a fraction of that.
"It really is going to be on a case by case basis. Change is going to impact the whole organisation - not just the guys in the tower - we'll have to start to be more resilient and more flexible to that change," he said.
"There may be some individuals who need to shift locations but that's not the goal of doing it - the goal of doing it is to create a more safe and resilient airspace."
New technology also allowed Airways to look at providing services in other countries.
"Things like virtual tower technology provides great opportunities because you can use that technology to look after a sector anywhere in the world quite easily. There's follow the sun services where we would work with European providers and do their night time operations at a better rate," said Fulcher.
Airways has more than 700 staff and provides coverage over 30 million square kilometres and manages more than one million air traffic movements a year.