Dropping bombs on cities is always going to kill civilians. When you say "Japan" I assume you mean Hiroshima and Nagasaki. The terrible destruction caused by those bombs has always caused a lot of controversy. One thing to remember is that no one knew, in advance, about radiation poisoning. In fact, a large group of scientists thought that detonating the bombs might cause a chain reaction which could destroy the earth. In other words, the aftereffects could not be predicted. The tests were done in the desert.
Many say that the targets had no military value. That's at best an urban legend and at worse an absolute fabrication. Hiroshima was headquarters for the Japanese 2nd Army, which commanded the defense of all of southern Japan. The city was a communications center, a storage point, and an assembly area for troops. It also had a heavy concentration of factories manufacturing munitions and other military goods.
From the Hiroshima Peace Memorial Museum website, a source with no reason to be biased in favor of the USA:
hiroshima.tomato.nu
Here is a map showing the military installations in and around Hiroshima:
hiroshima.tomato.nu
Why Hiroshima was chosen:
>>The size and the shape of the city was suited to the destructive power of the A-bombs. Because Hiroshima had not been bombed, ascertaining the effects of the A-bomb would be relatively easy.
Hiroshima had a high concentration of troops, military facilities and military factories that had not yet been subject to significant damage.<<
hiroshima.tomato.nu
The second bomb, detonated on August 9, 1945, was destined for Kokura Arsenal on the southwest Japanese island of Kyushu. Due to bad weather, the pilot instead bombed Nagasaki, the home of a Mitsubishi torpedo factory.
The reasons for chosing the second targets:
>>The two target cities had been carefully selected. They had purposely not been bombed
heavily by LeMay's B-29s so that, as the after-action report noted, "The assessment of the
atomic bomb damage would not be confused by having to eliminate previous incendiary or
high explosive damage."
Kokura, on the northeast corner of Kyushu, was chosen as the primary target for Fat
Man because it was the enemy's principal production source for automatic weapons. It
was also the site of the Mitsubishi Steel and Arms Works and was one of the largest
shipbuilding and naval centers in Japan.
Nagasaki, the secondary target, was the third largest city on Kyushu. It was also one of
Japan's leading shipbuilding and repair centers. It was not considered a completely "virgin"
target, however, because it had been bombed many weeks before by Twentieth Air Force
bombers. Niigata was originally considered as a third target, but it was too far away from
the other two cities. <<
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