The fundamental issue here is that the intelligence community plots political conspiracies to direct governments in their favors, even plotting against their own government to be controlled for the maintenance of their power.
In the Japanese case, the Japanese intelligence and CIA are the main powers to affect the government decision unnecessarily, which are associated with their asset, including the left extremist. Although, they have factions and sects inside the intelligence community, which hold different opinions to each other. Some intelligence sub-group closely works with the extremist, but others should loathe them just to be held as the asset to know the detail of their illegal activity. This division should be the same to CIA that there are several chains of the command, along with the independent conspiracy conducted by the asset, whose disorder creates a devastating result.
The neighbors also affect Japanese society and policy, including the most radicalized North Korea, which has a deep tie with the left extremist. They actually have conducted devastating plots in Japan, which is more than you assume, as the majority of them are not open to the public. At the same time, there are hidden followers outside the known left extremist still to pursue the revolution, which is partially supported by Japanese intelligence as well. This complicity makes it harder to judge who is in charge and who is responsible for the illegal action.
It is not just happening in Japan, but in the US and Europe as well. There are various criminal activities conducted by the intelligence community, including the murder. Their assets plot their own conspiracy and commit a crime for their sake, which often leave untouched even if found, as they are occasionally exempted from the criminal charge, as an intelligence asset. Or, they sometimes add another plot to disguise the first, which makes the situation worse, with more casualties. As a result, the conspiracy is filled with lies and manipulations, which requires additional plots to cover, failing the country, again and again.
This kind of mess has been continued for a long time, which is not known to the public partially because of the technology to conceal the intelligence trail. Actually, some of the plots including the murder and other criminal activities are hard to be proven due to its technology, which is necessary to be understood to resolve the current disorder of the intelligence community.