The issue is who fell helicopters down. Basically, the electromagnetic manipulation is conducted by the CIA and Japanese police intelligence in Japan. These attacks might be executed by the CIA, though it looks like the outcomes were beyond their capability.
The CIA officers have been understaffed to conduct this kind of operations, hence these would have been conducted by the CIA assets if that were the case. However, these events were geographically deviated to run the same chain of their command.
For example, if you target the helicopter in Sendai, a northern city of Japan, you need to understand the general flying route, analyze the best location for its operation and wait until it actually follows suit in that way. The CIA can send a team there for its research and action, but they cannot run this operation, two months after completing the first mission in Wakayama, at a middle of Japan.
These attacks were more like driven by a domestic group targeting helicopters of the defense force. Moreover, there had been several mysterious accidents in Wakayama for months until then, which was likely conducted by the same group. They also have their perpetrators located in Sendai, which was why these attacks were executed completely in the same way. Even if they used the same device, the local should have done a research for the attack.
The police intelligence might conduct these operations, though there is no reason for them to attack these helicopters. The defense force had already known the electromagnetic wave until then and fully realized the police intelligence has its capability.
Actually, some of the agents at the defense intelligence have been from the police intelligence, so that they cannot target the military helicopters apparently like this. I cannot dismiss its possibility, but it is quite less likely.
There is another perspective on these events that a control over the bird is not general. I actually saw many times that birds were manipulated electromagnetically, but I also heard not all the manipulators had the capability to maneuver the bird. As you can imagine, the bird cannot be controlled by the human language, therefore its control should be 100% conducted by the emotional manipulation. That is why the limited number of perpetrators have this capability and the suspect might be narrowed down for these attacks.