MPI compliance director Dean Baigent said the ministry had been gathering information on black market fishing and trading in Hawkes Bay since March 2014.
He said during this time a special duties officer for MPI became involved in the black market activities.
Commercial fishing premises in Hastings and Napier were being investigated due to their suspected involvement in the illegal trade of shell fish.
Mr Baigent said the theft of paua and crayfish undermined the sustainability of both fisheries, putting them at risk for genuine fishers, whether they were customary, commercial or recreational.
"It is MPI's role to ensure people are fishing by the rules and to protect New Zealand's fisheries for future generations. As this operation would indicate, it is something we take very seriously."
It is illegal to sell a recreational fishing catch with a maximum penalty of five years imprisonment and/or a $250,000 fine.