"We haven't done patching to this extent before - the fundamental reason is that we've seen huge growth."
It was not yet wide enough for aircraft to taxi to the side of the runway and this put more pressure on the main runway.
In the 12 months to the end of May, the airport had 1.39 million passenger movements, up 11.5 per cent on the previous period.
New Zealand Airline Pilots Association technical director Captain Rob Torenvlied said pilots had expressed concerns about the state of the runway earlier this year. Some ruts were deeper than 12mm.
"What was happening in Queenstown was that [we were] getting ruts in the centre line. Heavy A320s and 737-800s were landing in the same spot and the ruts were preventing water from running off," Torenvlied said.
Fuel in Queenstown is expensive so airlines "tanker" it in.
"They arrive with as much fuel as they can to minimise fuel uplift in Queenstown - it's a common practice but they're landing at near maximum weight."
The patching appeared to have alleviated the problem.
"We're keeping a very close watching brief on it and regularly get feedback from our members."
Queenstown was a challenging runway.
It was relatively short and narrow and subject to "wicked" wind effects at times, Torenvlied said.
The airport has been given approval for after dark operations on the condition it widens the runway from 30m to 45m.
Last year, it said the work would cost around $10 million.
Clay said the entire runway would be resurfaced at that time, making the entire area harder and more durable.
The widening and resurfacing work would be done at night to avoid disruption to flights.
Airport ownership
• 75.1% by Queenstown Lakes District Council.
• 24.9% by Auckland International Airport.