The Swiss filed 832 applications per million inhabitants last year, the office said in a report released on Thursday.
Although this level was down two percent from the previous year, it remained well ahead of the nearest competitors, Sweden (402), Finland (360), Denmark and the Netherlands (both 347).
ABB headed the list of Swiss companies filing patents with 455 applications, followed by Nestlé (435), Alstom SA (367), drugmaker Hoffmann-La Roche (360) and Novartis (281).
It was not just companies involved but universities with incubators for start-up companies, the EPO report shows.
ETH Zurich, the Federal Institute of Technology, made 68 applications, while the University of Zurich made 44 and the Ecole Polytechnique Fédérale de Lausanne (EPFL) 38.
Overall patent filings in Europe grew by 2.8 percent to reach an all-time high of 266,000, up from 258,000 in 2012, the EPO said.
Almost two-thirds of the applications to the office came from countries outside Europe, with the EPO’s 38 member states accounting for 35 percent of filings, it said.
The average for the 28-country European Union was 129, compared with 177 in Japan, 107 in the US and China (3), according to the report.
"Demand for patent protection in Europe is up for the fourth consecutive year," EPO President Benoît Battistelli said in a statement.
"This is proof that companies from around the world continue to see Europe more and more as a premier hub for innovation,” Battistelli said.
“The strong position of European companies in patent-intense technologies also underlines the central role these industry sectors play in generating employment and growth in the EU economy."