District council general manager property Leighton Toy said staff had been involved in managing the smouldering material with heavy machinery and assistance from the fire service.
Meanwhile, Horizons consents monitoring team leader Pita Kinaston said Natural Earth Solutions had not followed its environmental management plan.
The four consent breaches include exceeding the maximum height of 3m, failing to keep accurate records of material coming on site; and failing to submit an annual monitoring report to Horizons.
"The site has been significantly non-complied and an abatement notice has been served to formalise an agreement with Natural Earth Solutions not to bring further material on site to be composted," Mr Kinaston said.
Horizons consents monitoring officers met Whanganui staff on Tuesday and reported the remediation work undertaken by the district council was going well.
The composting site has been smouldering since March when the fire service was called to the site after it spontaneously ignited.
Natural Earth Solutions director Dave Towers said the company would not comment until it had concluded discussions with the two councils.