THE pharmaceutical industry in Europe last night welcomed the overwhelming endorsement by Euro MPs in Strasbourg of legislation which will allow them to patent biotechnological inventions.

The outcome was a complete reversal of the European Parliament's stance three years ago, when MEPs rejected similar legislation because they believed it failed to take sufficient account of the ethical questions raised by such scientific inventions.

The new rules, which expressly forbid any cloning or patenting of parts of the human body, embryos, or a sequence of genes, will now be formally rubber-stamped by EU governments later this month and take effect within two years.

Supporters of the legislation believe the legal protection it will give to biotech inventions will encourage drug companies to invest in research in remedies for illnesses such as cystic fibrosis, which are currently incurable.

They successfully argued that not only would medical advances be encouraged but that jobs would be created.

Mr David Earnshaw, the director of government affairs at SmithKline Beecham, said yesterday: ''The vote is good for medical research and therefore good for patients. It is good for European jobs and therefore for inventions. It will lead to new medicines, new vaccines, and new diagnostics.''

With 432 MEPs supporting the new rules and only 78 opposing them, the outcome was a conclusive end to a 10-year debate which had reached unusually high levels of passion and bitterness and involved intensive lobbying by drug companies, patients' groups, and environmentalists.

Yesterday, Green MEPs staged a last-minute protest by dressing up as pirates with eye-patches and displaying a banner proclaiming: ''No to bio-piracy'', in the Strasbourg debating chamber.

However, despite the heat generated, the complex legislation was passed unamended yesterday, after efforts to strengthen protection for animals and to ensure that farmers could use genetically modified seeds without having to pay royalties to the company which had invented them, had been rejected.

While Labour MEPs supported the legislation, it was unsuccessfully opposed by the SNP's two Euro MPs. The Highlands and Islands Member, Mrs Winnie Ewing, complained it ''debased the currency of humanity'' and would give ''carte blanche to multinationals' profit motive in the pharmaceutical sector''.

The heavy defeat left critics of the patenting legislation dismayed and they accused MEPs of championing commercial interests over ethical values.

''Bio-piracy - the unauthorised patenting of genetic resources taken from developing countries by mighty Western multinationals and institutions will not be stopped,'' warned Belgian Green member Magda Alvoet.