The amendments also could make it difficult for the directive to complete its journey through the European Union's Byzantine lawmaking procedures, with Commissioner Frits Bolkestein threatening to kill it in favor of negotiating an intergovernmental treaty that would require no democratic scrutiny.
The text was approved on its first reading with 364 in favor, 153 against and 33 abstentions.
The so-called Directive on the Patentability of Computer-Implemented Inventions was presented as a technical adjustment to harmonize 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 existing law blocks from being patented. The directive, its proponents argued, would clarify what could and could not be patented, offering clarity for businesses.
The proposal was, software developers, economists and corporations as failing to clearly define patent limits, and thus allowing any software to be patented.
The directive was passed with several amendments that had been supported by critics. One amendment, its advocates said, more clearly defines what can be patented and what cannot. Another allows a patented technique to be used without authorization or royalty payments if it is needed solely to ensure interoperability.
The latter exemption was opposed by a representative of the U.S. 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 criticized 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 harmonization 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.
If the directive passes through the rest of the EU's decision procedure, member states will be required to implement it in local law.
ZDNet UK's Matthew Broersma reported from London.