The polite reminder comes as Prime Minister Shinzo Abe is preparing to issue a statement to mark the 70th anniversary of Japan's defeat in World War Two, the legacy of which still plagues Tokyo's ties with China and South Korea.
The statement will be closely watched by Beijing and Seoul, which suffered under Japanese militarism, as well as Tokyo's close ally, Washington.
Abe has said he intends to express remorse over the war and that his cabinet upholds past apologies, including the landmark 1995 statement by then-premier Tomiichi Murayama. But it is unclear whether Abe will repeat the "heartfelt apology" and reference to "colonial rule and aggression" in that statement.
In a speech at the start of her first visit to Japan since 2008, Merkel referred to a 1985 speech by the late German president Richard von Weizsaecker in which he called the end of World War Two in Europe a "day of liberation" and said those who closed their eyes to the past were "blind to the present".
Merkel said Germany still appreciates the generosity of its neighbors that accepted the country back to the international community despite the horrors of the war and Holocaust.
"Without these generous gestures of our neighbors this would not have been possible. There was, however, also a readiness in Germany to face our history openly and squarely," she said. "It's difficult for me as a German chancellor to give you advice for how to deal with your neighborhood. It has to come out of a process in society."
Feuds over wartime history as well as territorial rows over disputed islands and geopolitical rivalry have frayed Tokyo's ties with Seoul and Beijing in recent years. Sino-Japanese relations have thawed a little since Abe met Chinese leader Xi Jinping last November but ties with Seoul remain frosty.
Some scholars say that while Japan bears part of the blame for East Asia's inability to lay the ghosts of the war to rest because its conservative politicians often cast doubt on the sincerity of past apologies, China and South Korea also keep tensions alive because history can be a useful political and diplomatic card.
Reuters and the Associated Press contributed to this report.