The CIA must be an organization to develop this electromagnetic wave technology, which is deployed in the US, but also around world including Japan.
There is a critical issue for the CIA that they are insufficiently staffed to conduct a large scale operation. There are more CIA officers in Japan within East Asia, but their size is still too small to run an operation to affect the Japanese society, which necessitates them to hire external capacity.
One of the methodologies to cope with this understaffed issue is to conduct a mission with other intelligence organizations of Five Eyes. They can avail some officers from other four countries, hence they can expand their capability. However, other organizations are by far smaller so that its support is still not enough at least in Japan.
The Japanese police intelligence is quite sizable, which can be used for their operation as well. Especially for this electromagnetic operation, this device itself should be provided by the CIA to them, hence they can easily employ them for their operations. However, they might have a different view on the political plot in some cases, which makes the CIA hesitant to use them for all occasions.
In any cases, the CIA asset is always the most available to them. Even if they hire some of ranking officers at the Japanese intelligence, they cannot control the whole organization for some cases. On the other hand, the direct CIA assets are always available for their any operations, which makes up their understaffed. In this way, they can conduct deeper and more widespread operations in Japan,
The CIA has several chains of command in Japan under the Asia desk. They have an office in Japan, which is a regional center to mainly conduct an operation in the region, but there are other members directed by other chains of command, based on the intelligence functionality.
It means there are multiple lines of operations in Japan, which is highly likely secretive each other. That is one of the reasons why there are several intentions for their operation even for the same subject. Adding to this, there are rogue agents and assets just working for their interests, which makes their operation more complicated.
This should be the same to any countries in Asia and probably in the US that their chain of command is ignored and abused often. That is one of the reasons why there is a political assassination highly likely not commanded by the US government but executed by CIA, sometimes with this electromagnetic wave operation.