This is an interview done with an IJN ace, Honda Minoru. In it, he discusses how he was convinced that he and his squadron could have destroyed Bockscar before it bombed Nagasaki. So with his testimony in mind: why weren't they sent up to attack?
https://www.youtube.com/watch?v=3H_9iR7zvMk (Hiroshima and Nagasaki at 9:58, description of attack method vs B-29's at 16:18)
You might be interested in past posts on the related topic of the Enola Gay's similarly unmolested flight to its target:
The Enola Gay was able to fly into Japan without resistance due to similar flights done by the US that were believed to be recon, but did these previous flights get attacked and did these men die without fighter support so that the Enola Gay could complete its mission?
^(13 May 2015 | 14 comments)
^(/u/DBHT14 attributes it the limited resources of the late-war Japanese Air Force.)
^In ^(this answer)^(, /u/Bigglesworth_ describes the reconnaissance flights and test runs which were taken over Japan in preparation for the bombing.)
How was it possible to fly a bomber into WWII Japan without anyone bothering them?
^(01 May 2013 | 28 comments)
^(/u/restricteddata describes the scale of US air operations in late-war Japan as well as Japanese responses these raids.)
The basic answer is found if you ask: How do you spot the one B-29 carrying an atomic bomb, as opposed to all of the other B-29s flying around?
At any given time during the war, there were solo or duo B-29s flying over Japan, making reconnaissance missions. Indeed, during the atomic bomb raids, a single B-29 scoped out each target city an hour ahead of time to see about the weather conditions (fun fact: the Enola Gay was the plane used to check the weather conditions over Kokura for the second atomic bomb strike, and reported good visibility — by the time Bockscar showed up, this was wrong, and they moved on to Nagasaki instead).
Japan had drastically limited fighter capability at the time. If they try to chase down every lone B-29, they would be spreading themselves very thin. B-29s would be making runs photographing cities and checking weather. The amount of reconnaissance at that phase of the war was high because the Americans had basically accomplished air superiority over Japan.
If the Japanese had known that Bockscar was carrying an atomic bomb, and could pick it out from all of the other B-29s (it was not labeled with anything "special" — in fact it carried the insignia of a different, random bomber group to make it hard to spot visually)... sure, they could have intercepted it. But over the days after the Hiroshima bombing, how many lone or duo B-29s were out there? Dozens. The Japanese wouldn't have been able to intercept them all, even if they had tried. That was part of the strategy of sending those planes against Japan with virtually no backup or defense — it would make it hard for anyone to defend themselves.