An expert in marine biology said the chances of the mussels surviving depended on a variety of factors but the chances were good given their quick return to the water from where they were taken.
MPI officers confirmed the vehicle, boat and trailer used by the men were confiscated at the scene.
The trio were allegedly obstructive with the compliance officers and police were called.
"This was a result of a very good call from a member of public who is to be commended for their efforts," said the compliance officers.
"This is an extreme breach of the recreational limits and this sort of behaviour is a clear threat to sustainability of our fisheries resources.
"Blatant offending of this nature will not be tolerated."
The men face serious Fisheries Act charges punishable by fines of up to $250,000 for the shellfish but also charges for obstructing fishery officers.
They will be summonsed to appear in the Whangarei District Court.
The mussels were returned to Whangarei Harbour on Thursday morning.
Canterbury University professor David Schiel, head of the marine ecology research group, said if the mussels were kept cool and out of the sun the chances of them surviving after being put back in the ocean were good.
"Mussels will last a long time if kept cool and in a wet sack," Mr Schiel said.
"If they get a day or two to settle and not be washed away with tidal currents they will reattach."
