The trip is the first visit to the city by a sitting American President since the world was first shown the potential key to its own destruction in a bombing that claimed the lives of 140,000 people.
Obama to make historic first presidential visit to Hiroshima
Chinese foreign minister Wang Yi said that the massacre of civilians by Japanese troops in the city of Nanjing deserved greater reflection.
"Hiroshima is worthy of attention. But even more so Nanjing should not be forgotten," the ministry's website cited him as saying.
"Victims deserve sympathy, but perpetrators should never shirk their responsibility," told a huddle of reporters, state broadcaster CCTV showed.
China says 300,000 people died in a six-week spree of killing, rape and destruction after the Japanese military entered Nanjing in 1937, although some respected academics put the number lower.
China historian Jonathan Spence, for example, estimates that 42,000 soldiers and citizens were killed and 20,000 women raped, many of whom later died.
The state-run China Daily newspaper declared in an editorial on Thursday that the "atomic bombings of Japan were of its own making".
It accused present-day Japanese officials of "trying to portray Japan as the victim of World War II rather than one of its major perpetrators".
Obama says no apology for A-bomb on Hiroshima visit
While some in Japan feel the attack was an abomination because it targeted civilians, many Americans and former allied countries say it hastened the end of a brutal and bloody conflict.
China's ruling Communist party often reminds its citizens of the brutal behaviour of Japanese soldiers who occupied China during the War, and accuses Tokyo of attempting to whitewash history.
The bombing of both Hiroshima and Nagasaki was justified, the China Daily said, as "a bid to bring an early end to the war and prevent protracted warfare from claiming even more lives".
"It was the war of aggression the Japanese militarist government launched against its neighbours and its refusal to accept its failure that had led to US dropping the atomic bombs," it added.
Obama's visit comes on the sidelines of a meeting of the Group of Seven nations in Japan, which on Thursday said it was "concerned" about rising tensions in the South China Sea.
Beijing said that the bloc of major economies -- which excludes China -- should stay out of its disputes with several Southeast Asian neighbours.
China's Communist party mouthpiece, the People's Daily, published a commentary Friday saying Japan had "disregarded the feelings of Asian countries, manipulated historical facts, abandoned peaceful promises, and created threats to the regional security situation".
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