Under the recreational fishing limit, people are only allowed to take 10 paua per day.
After the paua had been seized and processed many were found to be under the 125mm legal size limit, MPI says.
The three men have been charged with serious fisheries offences that carry a possible sentence of up to five years in prison, or a $250,000 fine.
MPI officers observed the group for some time before finding the stash and saw two of the men using a small motorised dingy in dangerous sea conditions to get paua they’d stashed earlier.
MPI’s Mike Green said he was disappointed to see people gathering paua on such a large scale and said it could take months if not years for the area to recover.
“Wellington is well known for its paua and in places there is a good and plentiful supply for all to enjoy.
“The actions of these individuals in this particular case go a long way to ruin that for everyone else.”
He urged anyone who saw suspicious fishing activity to get in touch with MPI.
The men are due to appear in Porirua District Court on November 11.