The traveller said his family had eaten the rest of the bat in Samoa and he wanted to show the head to his relatives in New Zealand.
Biosecurity New Zealand says the head was in a poor condition - partly mummified with loose flaps of skin.
Passenger manager Craig Hughes says they've seen some strange things from passengers and this incident is definitely up there on the list.
"It was a biosecurity nightmare. Bats have a terrible reputation as disease carriers and the remains could have harboured hitchhiker pests."
The bat's head has been destroyed.