A single seed contains enough abrin toxin to kill an adult, although its hard shell allows it to be handled or even swallowed without releasing the poison, a MPI statement said.
"It's standard practice for MPI to x-ray hollow handicrafts for seeds and other contaminants that could wreak havoc on New Zealand's natural resources," said Craig Hughes, MPI manager north, passenger and mail.
"We often find seeds and plant material, but something like crab's eye is more unusual, although we occasionally find seeds of this type on handicrafts from Africa and the Caribbean."
Crab's eye is an invasive pest in many tropical regions, including parts of Australia.
"It is clearly something we don't want in this country," Mr Hughes said.
"The passengers deserve a big thank you for considering New Zealand's biosecurity needs when they filled in their declaration cards."
MPI removed the seeds from the maracas before returning them to the passengers.