The Greenpeace ship, Rainbow Warrior, claims there are many illegal foreign fishing vessels visiting Suva harbour.
Radio Fiji reports that this is disclosed in a dossier of such vessels fishing in Fiji and the rest of the Pacific.
The Greenpeace oceans campaigner, Pio Manoa, says these vessels are disregarding regional registry compliance and taking advantage of Fiji's ports to get their illegal catches into foreign markets.
Mr Manoa took Fiji journalists on a tour of Suva harbour and showed them three vessels which are not registered with the Forum Fisheries Agency which implements the mandatory vessel monitoring scheme.
The vessels had flags from Cambodia and Equatorial Guinea , countries whose products are banned in Europe because they are notorious for non-compliance.
Greenpeace has called on Fiji authorities to investigate these pirate vessels.
Greenpeace says many of these vessels keep changing their names and call signs, which Fiji Fish managing director Graham Southwick says is common industry knowledge.
It estimates that Pacific island countries lose between 135- to 700-million dollars a year to illegal fishing, a sum more than they earn in access and licence fees.
The fisheries minister, Konisi Yabaki, says it is up to border control agencies like customs and the navy to monitor these vessels.