Speaking in Brussels on Tuesday, maritime and fisheries commissioner Maria Damanaki, said, "We are convinced that these two countries exercise no real control on what goes on in their waters and on their ships.
"So they cannot guarantee that their fish is caught respecting local and international rules," she argued, adding, "Any illegally caught fish is of great concern to me: it undermines the livelihood of fishing communities and depletes fish stocks."
According to the commissioner, two thirds of the fish consumed in the EU is imported, and "half of the tunas caught in the Pacific end up on our plates here in Europe".
"Any illegally caught fish is of great concern to me: it undermines the livelihood of fishing communities and depletes fish stocks" - Maria Damanaki
"So what is happening there is our business too. Sustainability of fisheries in the Pacific Ocean means sustainability here," explained Damanaki.
However, the Greek official continued, "Sustainability remains a 'paper tiger' if each segment of the fish supply chain is not taking full responsibility: from flag states to market states, from producers to importers, from inspectors to consumers."
She was keen to stress that the "warning is not the end of the road" and that over the coming months the commission will "intensify and formalise dialogue".
"We propose to each of them a tailored "action plan" to help them overcome their shortcomings," added the commissioner.
This approach was used in 2012 when eight countries were warned over their fishing practices, and the commission saw progress in five of the countries.
However, Guinea, Belize and Cambodia were banned from trading fish into the EU in March this year due to their lack of action in tackling the problem.
"I urge the Philippines and Papua New Guinea to take action so that this second step will not be necessary," said Damankai.
In closing, the commissioner called on other nations to "join us in tackling this plague of illegal fishing".
Xavier Pastor, executive director of Oceana in Europe, responded to the news, saying, "The EU commission confirmed its dedication to the fight against [illegal, unreported and unregulated fishing (IUU)] , sending a strong message that their previous actions to tackle IUU were not singular acts but part of a long-term policy.
"It is now up to the Filipino and Papuan governments to radically improve and take a strong stance against IUU activities in their waters and by their fleet. Disrupting this destructive activity will improve local fishermen’s livelihoods and increase fish stocks," he said.
Meanwhile, Eszter Hidas, EU policy lead for WWF's Transparent seas project, argued, "This is not an exercise in singling out nations but rather, an exercise in enforcing effective implementation of international fishing laws and regulations.
"There must be consequences for those who continually avoid playing by the rules" - Eszter Hidas
"There must be consequences for those who continually avoid playing by the rules."
She continued, "Eliminating the multi-billion euro business of IUU fishing worldwide needs a concerted and global effort.
"Leading seafood market states such as the EU, US and Japan must establish equally effective barriers to keep illegally caught fish out of their markets and thus jointly discourage illegal fishing activities worldwide," she finished.