The discord has emerged since the 27-country bloc adopted its new Lisbon Treaty late last year, which sowed confusion by empowering a new European Council president and foreign policy chief.
"We're in a bit of a mess," one senior EU official said on Friday (21 May). "We're still feeling our way forward."
The first sign of the EU's new impotence emerged at the last meeting of the Convention on International Trade in Endangered Species (CITES) in March, when EU countries struggled to find a common voice on protecting the Atlantic bluefin tuna.
Bluefin populations have been cut by 80% in 40 years, largely to satisfy sushi lovers in Japan, and EU governments agreed in March to support a trade ban to protect the fish (EurActiv 11/03/10).
But while Japan lobbied hard and early against a ban, Europe was so embroiled in internal wrangling and so inflexible in its approach that it failed to make an impact (EurActiv 19/03/10).
"There are lessons to be learned from CITES," said European Commission environment spokesman Joe Hennon. "The EU needs to be in a position to engage with international partners and to do so early enough to make a difference."
The EU was left feeling as powerless at CITES as it did when it came away empty-handed from climate talks in Copenhagen last December, a meeting at which it had hoped to lead the world to a strong global deal on cutting climate-warming emissions.
Opponents of whaling now fear the same confusion could help those who want to legitimise the hunt.
Whale hunting was banned in 1986, but Norway, Japan and Iceland have used loopholes to kill thousands of whales since then. The International Whaling Commission (IWC) will discuss a proposal in June that would reduce the catch but at the same time legitimise it.
At a March meeting of the IWC, EU countries were confused about how to vote on the hunting of humpback whales off Greenland, because Denmark supported the hunt and there was little chance of finding a united EU stance.
"This absurd position [...] effectively means that one member state can block the conservation efforts of all other EU member states in international fora like the IWC, CITES and other environmental treaty meetings," said Chris Butler Stroud, of the Whale and Dolphin Conservation Society (WDCS).
"This is a backdoor hijacking of democracy and the rights of governments to represent the European people's strong anti-whaling stance," he added. Lawyers have advised the WDCS, however, that despite the advice member states are receiving, the new EU treaty has not robbed them of the right to vote.
Battle over mercury
Meanwhile, the political battle over who speaks for the EU continues in its Brussels headquarters.
The European Commission last week rejected a proposal that it share responsibilities with EU member states at United Nations talks on mercury pollution in Stockholm in June.
Member states are worried it would set a precedent for other negotiations.
The row escalated this week when the Commission withdrew its own proposal, leaving the EU without a common stance to take to Stockholm.
"The Commission is looking for a mandate on mercury," said environment spokesman Hennon. "We regret how things have gone."
Greenpeace urged the EU to resolve the issue and lead global environment talks from the front.
"It's the Commission's job to sort this out or it risks undermining the whole purpose of the EU," said Greenpeace spokesman Mark Breddy.
(EurActiv with Reuters.)