On inspection they found signs of previous and current excavation work of the lava flow, the construction of a rock wall and the removal of protected plants and trees.
The property owner was asked to stop works but continued until a formal enforcement notice was issued against him.
After further investigation, Auckland Council decided to lay charges, which resulted in a a $16,250 fine imposed by the District Court.
Auckland Council consenting spokesman Mark White said the ecosystem was nationally significant and local residents were protective of the special area.
"However in this case, it was being damaged and enforcement measures were needed to protect the environment from further destruction."
The council's resource consent process enabled the council to limit the environmental impact of proposed development works, or avoid the most ecologically sensitive areas, Mr White said.
Lava flow forests were rare, occurring when vegetation grew on lava rock left from volcanic eruptions.
The Almorah forest was the largest remaining area of lava flow forest in central Auckland and had been identified as a significant ecological area in the council's Isthmus District Plan and the Proposed Auckland Unitary Plan.
A resource consent application proposing extensive mitigation work at the Epsom property, including restorative landscaping, was currently being processed by the council.