Part of the widespread investigations involved officers, along with a police photographer, spending several hours at the HB Seafoods site in Ahuriri, although no comment was being made at this stage on any involvement by the company.
MPI compliance director Dean Baigent said Operation River had been gathering information on black-market fishing and trading in Hawke's Bay since March last year.
"During this time an MPI special duties officer became involved in the black-market activities," Mr Baigent said.
"The officer uncovered illegal trading of paua and crayfish which had been gathered by recreational fishers, some of whom disguised their activities through the use of customary authorisations."
Customary authorisations are issued by local tangata kaitiaki/tiaki but must not be used for financial benefit.
Mr Baigent said the commercial fishing premises in Hastings and Napier were being investigated due to their "suspected involvement" in the illegal trade of shellfish.
He described the theft of paua and crayfish as undermining 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," he said.
"As this operation would indicate, it is something we take very seriously."
Mr Baigent says MPI has been aware of black-market activity within the recreational and commercial sectors in the Hawke's Bay region for several years. Operation River was planned and implemented specifically to target it.
"Black-market trading is very difficult to counter with traditional enforcement methods - the theft of seafood and its subsequent sale often happens below the radar and we have to use different tactics to apprehend those involved."
Under current laws, it is illegal to sell a recreational fishing catch with a maximum penalty of five years' imprisonment and/or a $250,000 fine.
Mr Baigent said MPI encouraged people to report any suspicious fishing, buying or selling by calling the confidential line - 0800 4 POACHER (0800 476 224).