About 60 minutes before the American bombers reached Hiroshima, they were detected by Japanese radar. Air raid warnings were sounded in several cities, including Hiroshima, but when it was determined that there were only three bombers, thus it was likely to be only a reconnaissance mission, some of the cities lifted the alarm. The Japanese military determined that aviation fuel was so precious that interceptors would not be launched just for three bombers. This might be caused from the regular visits that the US Army had been sending for the very purpose of making the Japanese lower their guards. from: http://ww2db.com/battle_spec.php?battle_id=49

The issues were technological and tactical.

Japanese aerial technology was always lagging. They produced some aircraft with exceptional abilities early in the war, but really the success of the Zero, Betty and Oscar (I will use Western call-names for simplicity) were the result of Western arrogance, refusal to deploy their best aircraft into Asia, the ability of Japanese designers to optimise their designs for the Pacific, and excellent training of the pre-war Japanese navy and army air forces.

Fast forward to 1944, and the Japanese industry was in crisis. The mix of technologies that made a good fighter in 1944 was simply beyond what the nation's industry could produce. These aircraft needed super- or turbo-charging, which in turn required the latest metallurgy and materials technology. Aerodynamic compromises possible in the first generation of monoplanes were not acceptable in the immediate pre-jet era, and things like radial engine cowlings and laminar flow wings required extensive testing and R and D. Even Japanese aviation fuel was of low octane due to limited industrial technology.

Japan's air forces ended the war mostly equipped with the same aircraft with which they started it: the A5M Zero and the Ki-43 Oscar. The replacements were either still in prolonged development, or had proven too unreliable to be really effective. The few aircraft that were 'good on paper' had limited success, usually due to engine problems or difficult maintenance.

And to employ all this tactically in air defence needed radar and radios to co-ordinate the defending fighters, and again Japan was way behind. In part this was due to the inherent limitations of late industrialisation, and in part because the Japanese military which controlled the entire society, had disdain for science and engineering and were confident that bushido warrior skill would always prevail.

What all this added up to on August 1945 was a grossly ineffective aerial defence. Even on good days earlier in the year, most Japanese fighters deployed to intercept incoming B-29s could not reach the operational ceiling of the Boeing, which it must be remembered represented the pinnacle of technological achievement in 1945 (capturing a crash-landed example, the Soviets were amazed and reverse-engineered a direct copy). Flying at around 300+ miles per hour, there was limited time for fighters to climb, deploy, and make attacks. A decent proportion of B-29 losses were the result of Japanese pilots simply colliding with B-29s, as many decided shooting at them was futile.

But this was during the heyday of the Japanese air defence (which compared to Germany's air defences were always pitiful). By August 1945 the Imperial Japanese Army and Navy had run out of skilled pilots, aviation fuel and oil, and skilled mechanics. Japan was mustering resources for an all-out defence of the homeland.

'B-29 Hunters of the JAAF' Henry Sakaida Ki-44 'Tojo' Aces of World War II' Nicholas Millman

Two things: One, the USAAF regularly used unescorted B-29s to do weather reconnaissance prior to raids. Even for the atomic bombing raids, this was done — an hour before the Enola Gay took off on August 6, there were single B-29s checking out Hiroshima, Nagasaki, and Kokura. There were probably other planes checking out other cities for other bombing and reconnaissance purposes.

Two, the magnitude of the air war on Japan at that point is staggering and easy to forget when we focus on the atomic bombings. Even without considering the incendiary raids. On the same day as the Hiroshima bombing, there was a raid of 150+ P-47s and A-26s attacking Miyakonojo, 170+ B-24s, B-25s, and P-47s hitting Kagoshima, and 100+ fighters from Iwo Jima attacking military installations around Tokyo. The day before Hiroshima, 330+ B-24s, B-25s, A-26s, P-47s, and P-51s attacked Tarumizu, and 470 B-29s flew incendiary raids against the cities of Saga, Mae Bashi, Imabari, Nishinomiya-Mikage. Another 106 bombed a coal factory in Ube, and another 27 mined the waters of Sakai, Yonago, Nakaumi Lagoon, Miyazu, Maizuru, Tsuruga, Obama, Najin and Geijitsu. 100+ P-51s hit military targets around Tokyo.

So the US is able to field hundreds of planes over multiple targets in Japan with near-impunity at that point. They are flying reconnaissance and weather missions all the time. The Japanese air force and defensive measures are tattered as it is; if they are going to do anything, they have to pick and choose very carefully. They can't exert an effort on every stray plane. And their odds of hitting any individual plane with AA is very low.