The EU issued the 'yellow card' after a pirate tuna vessel was busted fishing in Papua New Guinea waters by the NGO three weeks ago.
This means Taiwan, which has the biggest fishing fleet in the Pacific, may face European sanctions and import bans if changes aren't made.
An oceans campaigner for Greenpeace, Karly Thomas, says Taiwan has too many boats flying its flag with too little control.
"Taiwan has more than 1,000 longliners operating in this region and for the fisheries agencies to start putting much more scrutiny on them and stopping them operating illegally is going to be of benefit to the legitimate fishing industry in Pacific island countries, because at the moment it's bad for everyone involved in the fisheries that this is going on."
The EU has lifted its 'yellow card' warning for Papua New Guinea, saying it has significantly reformed its fisheries governance.