Martek said the patent which has been broken is European Patent No. 0
515 460 relating to microbial oils containing at least 35 per cent DHA (docosahexaenoic acid).
Judges in Dusseldorf, Germany, this week gave a verbal ruling in favour of Martek.
A written judgement is expected in 30 days.
A spokesperson for the Swiss firm Dominik Werner told NutraIngredients.com that the firm was disappointed with the judgement and will do everything it can to fight back.
He said: "Lonza has submitted extensive data, which it believes offer suitable evidence that Lonza has not committed any patent infringement.
"Lonza intends to lodge an appeal against the judgment and will exhaust all the remedies available under patent law in order to take action against the litigious patent ."
Werner added that the ruling will impact on sales of DHA in Germany, but other European countries will not be affected as there are no legal proceedings against Lonza elsewhere.
He said " the slight sales reductions " will not affect Lonza's short, mid and long term performance.
With the European omega-3 market expected to see growth of eight per cent a year until 2010, protecting company's interests and copyrights are of paramount importance.
According to the latest Frost & Sullivan figures, the European omega-3 market was worth around €160m (£108m) in 2004.
In the past five years more than 3,000 products containing omega-3 fatty acids have been launched worldwide, with Europe dominating the market, according to Mintel's Global New Product Database.
In the three years between 2003 and 2006, European launches increased from 61 to 404.
Omega-3 fatty acids have been linked to a wide-range of health benefits, including reduced risk of cardiovascular disease (CVD) and certain cancers, good development of a baby during pregnancy, joint health, and improved behaviour and mood.
Lonza DHA was sold for use in functional foods and dietary supplements.
The patent infringed by Lonza has been the subject of opposition proceedings at the European Patent Office since 1999 and a final resolution of those proceedings is expected at some time in the second half of 2008.
In October 2006, a jury in a U.S. federal district court in Delaware determined that Lonza's DHA activities in the functional food and dietary supplement areas infringed three U.S. Martek patents, an announcement said on Martek's website.
Martek chief executive Steve Dublin said: " We are very pleased that the court found that the actions of Lonza infringe this European DHA patent of Martek.
The decision further demonstrates both the company's resolve to vigorously defend its intellectual property portfolio and the strength of Martek's patent portfolio in the marketplace."
Martek has also filed patent infringement suits against Celanese Ventures GmbH and Nutrinova Nutrition Specialties & Food Ingredients GmbH.