I saw a documentary on TV regarding this. They said that the Japanese intelligence had knowledge that something along the lines of an atomic bomb would be dropped over Hiroshima. Why was no alarm raised? On the TV they noted this aspect but offered no explanation (they said no one knew why - (but I know reddit thinks otherwise) )
I've seen no credible source that suggests the Japanese had any kind of intelligence of this sort. Japanese intelligence was not especially accomplished when it came to the United States. Neither the Germans, nor the Japanese, had any good evidence of the US atomic bomb project, though the Germans did occasionally get rumors. There were many rumors on all sides about wonder weapons, however, and separating fact from fiction was non-trivially difficult.
(Also, it was a B-29, not a B-52.)
63 millions of leaflets were dropped on 35 cities of Japan five days in advance, and the radio in Saipan broadcast a similar message every 15 minutes, warning citizens that the cities would be bombed to destroy their war industries. "Since bombs don't have eyes," the citizens were begged to evacuate the cities for their own safety.
It was only after Hiroshima that leaflets spoke of the new "atomic bombs" that permitted one plane to destroy like thousands of bombers.
Security around the atomic project was very tight. While scientists had discussed the possibility of atomic weapons, it was generally considered not yet practical.