Counsel for MFL Kimberly Jarvis said her client had not known such actions were illegal.
It was not a case of the tyres being burned to save the cost of disposing of them properly, she stressed.
"I find that a bit surprising," Judge Brian Dwyer said.
"Common sense tells you tyres aren't a good thing to be burned ... I would've thought it would be pretty common knowledge."
Duncan had called Fire and Emergency New Zealand (Fenz) to inquire about burning the vegetation but did not inform Fenz of his intention to throw the tyres on, the court heard.
A member of the public complained to the council after witnessing the black smoke from the blaze.
Fenz was also alerted later that evening by police at Dunedin Airport and attended the scene.
The burn continued throughout the night and a council compliance inspector visited the property the next day.
He observed the piles in an old lane-way between two paddocks and, on closer inspection, noted "substantial amount of material from automotive tyres, including metal bands and belt braids".
"It must be recognised that the burning of tyres is inherently bad practice because of the toxic-component nature of the materials," Judge Dwyer said.
He fined MFL $5600 and imposed solicitors' and court costs.