However, the amendments could also make it difficult for the directive to complete its journey through the EU's Byzantine lawmaking procedures, with Commissioner Frits Bolkestein threatening to kill it in favour of negotiating an inter-governmental treaty that would require no democratic scrutiny.
The text was approved on its first reading with 364 in favour, 153 against and 33 abstentions.
The Directive on the Patentability of Computer-Implemented Inventions was presented as a technical adjustment to harmonise the way patents are treated by national governments across the EU. It seeks to correct a current problem whereby patents may be granted by the European Patent Office, but not enforced in member states, because they cover software or business processes, which are blocked from patenting by existing law. The directive, its proponents argued, would clarify what could and could not be patented, offering clarity for businesses.
It was criticised by small-business groups, software developers, economists and corporations as failing to clearly define patentability limits, and thus allowing any software to be patented.
The directive was passed with several amendments that had been supported by critics. One amendment was said by its advocates to more clearly define what is patentable and what is not. Another allows a patented technique to be used without authorisation or royalty payments if it is needed solely to ensure interoperability.
The latter exemption, Article 6a, was opposed by a representative of the US State Department in a recent position paper to the EU leaked by activists.
On Tuesday, in a debate ahead of the vote, Commissioner Bolkestein also criticised the amendments, telling the Parliament that "the majority of those amendments will be unacceptable to the Commission". He said if the "unacceptable" amendments were passed, the Commission could withdraw the Directive entirely and seek to achieve patent harmonisation through a renegotiation of the European Patent Convention.
"If I may be blunt... the process of renegotiation of the European Patent Convention would not require any contribution from this Parliament," Bolkestein told the Parliament.
The Foundation for a Free Information Infrastructure, which had campaigned for the amendments, applauded the result. "Now we will have to see whether the European Commission is committed to 'harmonisation and clarification', or only to patent owner interests," said FFII's Hartmut Pilch. "Yesterday's threats uttered by Bolkestein against the European Parliament suggest the latter."
Labour MEP Arlene McCarthy, who was responsible for guiding the directive through Parliament, also welcomed the result, while criticising those who had campaigned for amendments. "Campaigners against patents for computer implemented-inventions risk seriously undermining European industry's interests by putting them at an extreme disadvantage in the global marketplace and putting at risk jobs in the growing software industry," she said in a statement
If the directive passes through the rest of the EU's codecision procedure, member states will be required to implement it in local law.