It was raining heavily when the leak - initially in liquid form which turned into a highly dangerous gas, according to emergency services - occurred, meaning rainwater which washed into the site's water storage ponds had high pH levels due to it meeting ammonia, the company said.
"We're putting that water through our wastewater treatment systems to neutralise it.
"Given the site is currently shut and undergoing maintenance anyway, we are not rushing this work. The safety of our communities, employees and the environment is our priority."
The situation did not impact the pay of any employee, the company said.
WorkSafe, the Waikato Regional Council and Fire & Emergency NZ have been involved with the situation.
The company did not respond to Herald questions about the location of the leak or the costs of the incident and its aftermath.
The new dairy season started on June 1 but milk production will be limited until calving is over next month.
Fonterra said the Te Rapa site, which employs 500 people full-time at the season's peak, is not scheduled to fully reopen for several weeks - depending on milk supply.
The Te Rapa site at Horotiu, north of Hamilton, is one of eight Fonterra processing sites in the Waikato.
At a recent hearing where it opposed a major housing and water adventure park development proposal in the area, Fonterra said the site was a critical asset with a replacement value of nearly $1 billion.
In the dairy season it operates 24/7 and processes more than 7.5 million litres of milk a day into milk powders and cream products.
A $20 million expansion of its cream processing plant was completed two years ago.