Air traffic controllers will also give priority take-offs and landings to larger and heavier aircraft, which burn the most fuel.
Boyle likened it to ramp signals at motorway on-ramps.
"In this case we're keeping the red light on longer than usual to keep things moving more smoothly along the main routes," Boyle said.
But the conservation measures will slow the overall network performance.
"Passengers may notice that they are held on the ground for longer than usual. This is because it is better to have aircraft holding on the ground with the engines off, rather than slowing down en-route and burning more fuel in the air."
Rough weather across the country over the past few days has put additional pressure on the aviation network.
Aviation fuel can't be pumped from Refining NZ to the Auckland Airport because the pipeline the refining company operates failed. It could be late next week before normal aviation fuel supplies resume.