"There are a lot of rules around what we carry and where we carry it, so the chances of actually getting overheating or a fire in that area is extremely low," he said.
"Staff are equipped with a detection system and it was that detection system that failed. It wasn't actually anything that went wrong with the cargo."
Every six months staff are required to do simulation training in Melbourne which covers the issue that occurred during Monday's flight.
Emeny said the airline will look at ways to mitigate the "false warning" from happening again.
"The aircrafts go through regular checks but, following on from this, we will carry out an investigation into what happened and why, but largely we already know because the aircraft wouldn't have been released for service unless we did."
The delay meant Monday afternoon's Whanganui to Auckland flight had to be cancelled.
Emeny said all passengers due to travel on the cancelled flight were reallocated to flights for the next day.