The EU executive "decided today to ask the European Court of Justice for a legal opinion to clarify that the ACTA agreement and its implementation must be fully compatible with freedom of expression and freedom of the internet," it said in a statement.
However, even at the highest levels in Brussels, officials are deeply divided over the accord, with the justice commissioner openly criticising the deal.
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The United States, Japan and Canada are among signatories to the Anti-Counterfeiting Trade Agreement (ACTA), but a number of mainly eastern European states have threatened not to ratify the treaty, which critics say could curtail Internet freedom.
The Commission has defended ACTA against accusations that it amounts to a witch hunt against individuals illegally downloading content and has vowed to try to keep the deal alive when it comes up for ratification later this month by the European Parliament.
"Let me be very clear: I share people's concern for these fundamental freedoms... especially over the freedom of the Internet," EU trade commissioner Karel De Gucht told a news conference in announcing the decision.
"This debate must be based upon facts, and not upon the misinformation and rumour that has dominated social media sites and blogs in recent weeks," he added.
A string of protests has drawn tens of thousands of citizens onto the streets of European cities over recent weekends.Hacker group Anonymous has also claimed responsibility for cyber-attacks including one reported on Wednesday in Greece, in protests against the treaty.
"The decision by the Commissioner was due to the 'people-power' of the tens of thousands who had called for ACTA to be scrapped," said Sergei Stanishev, head of the Party of European Socialists in the European Parliament.
De Gucht said the agreement "aims to raise global standards for intellectual property rights" and that it "will help protect jobs currently lost because counterfeited, pirated goods worth 200 billion euros are currently floating around."
However, moments before De Gucht stood up to announce the move at a press conference, Viviane Reding, the commissioner for justice, fundamental rights and citizenship, criticised the deal.
Flagged up on Twitter, she said in a statement of her own that "copyright protection can never be a justification for eliminating freedom of expression or freedom of information."
She underlined: "That is why for me, blocking the Internet is never an option."
Twenty-two of the 27 EU states signed the Anti-Counterfeiting Trade Agreement (ACTA) on January 26 in Tokyo.
Since then, Bulgaria, the Czech Republic, Germany, Latvia, Lithuania, Poland and Romania have said they will not ratify the pact.
Slovenia's newly-appointed government also said last week it was considering freezing its ratification of the accord signed by the previous government in January.
EU Parliament president Martin Schulz has called the pact "unbalanced" and difficult to accept in its current form, and Organisation for Security and Cooperation in Europe (OSCE) media freedom representative Dunja Mijatovic said last week it could undermine freedom of expression.
