"The boots posed high biosecurity risk to New Zealand,'' said ministry team manager Paul Ruttley.
"If they had only been used on the street in the city, it would have been okay.
"But, as they came from a farm, they could have been carrying diseases with potential to have a devastating impact on our farming industries.''
The man was fined $400 for failing to declare biosecurity risk goods and the snail was "euthanised'', the ministry said.
Mr Ruttley says it is fairly common for MPI quarantine inspectors to intercept dirty boots, but very unusual to discover a hitch-hiking snail.
Cane toads from Australia have been found inside boots in the past, he said.