The German chancellor said her meeting with Prime Minister Shinzo Abe was "between two national leaders who want to work together, who believe that there can be very good win-win situations when all partners work together".
She added that February 1, when the free-trade agreement between the European Union and Japan came into force, was a "special day" which has "shown that we are prepared to make agreements -- even if multilateral agreements are to some extent in choppy waters".
The accord is the biggest bilateral trade deal ever signed, covering more than 630 million people and nearly one-third of global gross domestic product.
Merkel also stressed the importance of "fairness" and "reciprocity" in trade agreements at the start of her two-day trip to Japan accompanied by a large business delegation.
For his part, Abe said the two countries would "cooperate closely towards maintaining and strengthening a free and open economic system".
The German chancellor will also meet Emperor Akihito just months before he is due to abdicate and the crown prince Naruhito.
Stressing the economic aspect of the trip, she will also address German and Japanese business leaders and visit an artificial intelligence laboratory operated by electronics giant NEC.