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The EU patent scheme (see 'Background') is backed by 25 members but viewed as discriminatory by Rome and Madrid.
In a statement, the Italian Foreign Ministry said it had lodged the complaint with the court to defend the values of the union against abuse.
The statement said the use of enhanced co-operation procedure was "never intended to be stretched to nullify the original aims of the European treaties".
Against the spirit of the single market
It added: "The use of enhanced co-operation within the patent sector is contrary to the spirit of the single market, because it tends to create division and distortion within the market, and will thus prejudice Italian businesses."
Supporters of a single EU patent say it is time for the Union to replace the current system, which forces firms to patent their designs in every one of the bloc's 27 member states and in 23 official languages, at huge expense.
It is the second time that the courts have waded in to the patent row. Before the enhanced co-operation procedure had been agreed by member states in March, the Luxembourg court ruled that the creation of a Community Patent Court would not be compatible with the provisions of EU law.
Ministers to discuss the move in June
Hungarian Deputy Economy Minister Zoltán Cséfalvay said competitiveness ministers would discuss the issue at a special meeting on 27 June in Luxembourg.
In respone, Internal Market Commissioner Michel Barnier said: "I am confident that the enhanced co-operation procedure presented by the Commission is not discriminatory. We are assured that Italian and Spanish business will suffer no discrimination."
Patent titles are currently granted by the European Patent Office (EPO), which was set up in 1977 and now covers 38 countries, including all EU member states.
However, the so-called 'European patent' offered by the EPO is in reality nothing more than a bundle of national patents, with each country having its own set of different rules.
The current situation results in significant costs and legal difficulties for companies that want to protect their inventions across all European countries.
On 15 February, the European Parliament gave its approval for member states to make use of the enhanced cooperation procedure for setting up a common patent system.
The agreement among 25 member states concerns the creation of the European patent – which in legal jargon is known as a "unitary patent title" – as well as the use of English, French and German as the three main working languages.
However, another potentially more difficult issue is not covered by the ministers' agreement. This concerns the idea of setting up a common jurisdiction system, including a tribunal to resolve legal disputes, for example concerning the scope of individual patents.
Before the agreement on enhanced co-operation had even been reached, on 8 March, the European Court of Justice ruled that the creation of a Community Patent Court would not be compatible with the provisions of EU law, thereby casting a shadow of doubt over plans to establish a Europe-wide patent system.
The Hungarian Presidency estimates that the direct consequence of a fragmented patent system add up to around €750 million of extra costs on European businesses every year.