The Department of Conservation issued a notice over the weekend, saying the toilets were almost at capacity at the Mueller Hut Route on Aoraki Mount Cook.
This meant the route was closed to day walkers. People with hut bookings can still use the track and toilet.
"There have been far more visitors than anticipated this summer so the tanks have filled up faster than expected," a spokesperson said.
"We estimate up to 250 visitors per day have been using the track on busy days."
A statement on the DOC website said: "We aim to empty the toilet tanks, and reopen the track to day walkers, as soon as possible. Exact timing will depend on when the required specialist equipment is available."
Federated Mountain Clubs Vice-President Allan Brent said hikers were frustrated and DOC should have sent a helicopter to empty the toilets.
"I think it could've been headed off a lot earlier," he said. "It was a very foreseeable issue, very obvious that a lot of folks would be going up to Mueller Hut and that they'd be using the loo."
"The solution of getting a helicopter up there could have been easily found in the budget, I'm sure."
"There's no question that it's under intense resource pressure," he said.
DOC couldn't say when the popular track would reopen, but said anyone who had bookings could still use the track and hut.
A spokesperson says the toilets will be emptied as soon as possible, but they had to wait for specialist equipment to be available.
In the meantime, it is encouraging hikers to try nearby tracks like Red Tarns, Hooker Track and, for the more experienced, Sefton Biv.
