"Germany is in favour of opening such talks with a view to reaching a free trade deal agreement" with Japan, she told a press conference.
The EU has already concluded such a deal with South Korea "and we should do the same with Japan," she added. "Of course, there are bound to be some difficult issues to be negotiated, for example in the automotive industry."
She said she expected to discuss the matter further with Japanese Prime Minister Naoto Kan on the sidelines of the G8 summit later this month in France.
EU officials hope to be able to announce the opening of trade talks with Japan at an EU-Japan summit on May 27 and 28.
Prompted by Britain, leaders of the 27-nation EU bloc in March called for the speedy launch of negotiations for a free trade agreement to aid recovery in disaster-struck Japan - but on the proviso that Tokyo move to lift restrictions to trade.
Trade ties have consistently shown a strong surplus in favour of Japan - the EU currently being Japan's third-biggest trade partner while Japan is Europe's fifth.