But it appears the extra screening has been limited to passengers on large Boeing jets operated by Air New Zealand, its subsidiary Freedom Air, and Qantas.
Aviation Security Service general manager Mark Everitt told a parliamentary select committee that after consulting the Civil Aviation Authority he made a decision to screen only jets with more than 90 seats.
He refused to give the reason for the decision while media were present.
This means smaller planes such as Saabs, Bandeirante and Metroliners would not be screened.
The four American planes hijacked by terrorists last week were Boeing 757s and 767s but carried only 38, 56, 81 and 58 passengers.
A spokeswoman for Transport Minister Mark Gosche last night referred questions about the decision back to Mr Everitt, who did not immediately return calls.
Christchurch-based aviation editor Les Bloxham said it was difficult to know why authorities had set the limit. But one reason may be that the smaller flights could not fly long distances - for example, they could not cross the Tasman. They also carried less fuel, which would reduce their explosive potential.
Since security had been boosted at domestic terminals, several passengers have been caught carrying banned items including guns, knives and gas canisters in their hand luggage.
Mr Bloxham said security around freight bound for the US had also been tightened. Cargo was being held in New Zealand warehouses for 48 hours before travelling to the US.
Mr Everitt said past reviews of domestic terminal security had found that the risk of a breach was low and the cost of boosting safety measures could not be justified.
"We need to have a balance in the level of inconvenience to travellers weighted against our primary concern of safety," he said.
Passengers had been very tolerant of minor delays caused by the temporary increase in security, said Mr Everitt. "The public seem to be lapping it up and want every bit of security they can get."
The corporate services manager for Crown-owned Aviation Security Services, Mark Williamson, said the number of passengers travelling had dropped in North Island cities but increased slightly in the south since the terrorist incident in the US. Overall, numbers were down by 2.6 per cent. About 4.6 per cent fewer passengers flew out of Auckland and Hamilton
Meanwhile, a letter from American Embassy charge d'affaires Philip Wall has told the Government to expect a formal request shortly from Washington for consultations on New Zealand's contribution to efforts to hunt out the perpetrators of last week's acts.
Helen Clark is offering greater intelligence sharing and the possible deployment of crack SAS troops as part of an American-led multinational force.
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