Capt Lyons was speaking on the first day of the American Association of Airways Executives conference in Queenstown, where about 70 delegates from across the world will spend two days discussing airport security in ever-changing times.
Capt Lyons told the Otago Daily Times "it is of concern" passenger screening in New Zealand was limited to only planes of more than 90 seats.
New Zealand parliamentary transport and industrial relations select committee chairman, MP David Bennett, said flights travelling between "main centres" and planes with more than 90 passengers went through "a much more detailed screening environment".
Smaller flights to and from provincial airports "don't have such strict screening requirements".
Mr Bennett referred to an incident in February 2008 when Somalian woman Asha Ali Abdille, then 33,allegedly attacked both pilots on an Eagle Airways flight 10 minutes after take-off from Blenheim.
She allegedly demanded the plane be flown to Australia, and attempted to take the controls. One pilot was cut in the leg, the other in the arm and a female passenger on board the plane was also injured.
Abdille was charged with attempted hijacking, one count of wounding one of the pilots with intent to cause grievous bodily harm and two counts of injuring with intent.
Her trial is to be held in April in Christchurch.
Mr Bennett said the incident highlighted the risk of not screening all passengers "but we have to consider the cost of screening".
A review of domestic aviation security in New Zealand, found the cost, estimated at $160 million over 10 years, "prohibitive".
Capt Lyons, a pilot with 33 years' experience, said up to $50 million of that would be capital investment, with the remaining amount the cost of screening passengers, he said.
That would equate to about $5 extra per passenger.
"Just to focus on large numbers rather than breaking it down to effectively costs per passenger [is misleading]."
While the NZAPA had a "great deal of confidence" in aviation security, the pilots' primary concern was "to run a safe operation" and the association would like to see all passengers screened, even if it were only occasionally for small aircraft.
New Zealand had eight "security designated airports" - Auckland, Hamilton, Rotorua, Palmerston North, Wellington, Christchurch, Dunedin and Queenstown - where passengers were screened.
However, at those airports passengers were "separated out" and only those flying on planes with 90 or more seats were screened, Capt Lyons said.
Given that many international visitors were expected for the 2011 Rugby World Cup, Capt Lyons said he was "sure" the Minister of Transport was "well aware" of any potential issues.
