Waikato Regional Council successfully sought a court order to stop a pig farm discharging effluent into a waterway north of Te Aroha but that has not stopped the problem.
A video taken by council staff on 2 August showed effluent overflowing from a holding tank into a stream.
Landowners have been warned that piggery effluent has entered the Patuwhao Stream which flows to the Waihou River.
Because of this, compliance manager Patrick Lynch said there would be faecal bacteria, ammonia and high nutrients in the water.
"We're urging landowners taking surface water downstream from this site to exercise caution until the risk has passed," he said.
On 4 August, the council was granted an interim enforcement order from the Environment Court due to alleged ongoing, uncontrolled and unauthorised discharges to both land and water.
However the council said since then it had responded to a further significant discharge of effluent reported on 7 August.
"Applying to the Environment Court for an interim enforcement order is unprecedented in this region, but we view the ongoing discharges at this site to be an emergency," Lynch said in a statement.
"They are having an extreme impact on the environment and community, which we feel necessitates such action under the Resource Management Act.
"This latest incident will form part of an active investigation by the council, and as such we're unable to provide any further information at this time."
The order requires the piggery company to cease discharging a contaminant onto land in circumstances which may result in it entering water.
To do this it needs to reduce stock numbers, reduce the level of effluent currently being stored, and explore lawful options for relocating pig effluent offsite.