I think I figured out who the human, referred as an "Eerie voice" in Narukami's story, who is working with the Malevolent entity really is. I think it is Detective Kurosawa.
Here is why I came to this conclusion: If you play Naoto's story, she is given an assignment by a man in the JSDF to spy on the Kirijo Group's "Shadow Operative." After the incident at the airport she is given a contact that is willing to leak information about the group; the man also said that the contact seems to have his own agenda. The contact is revealed to be Detective Kurosawa, the same man who help P3's MC with supply against the shadows when he was just an officer, and takes Naoto to where Mitsuru and the others are located. Kurosawa goes up to them, surprising Aigis since that was not the original rendezvous point and he shouldn't have know where they were. Kurosawa debriefs his findings of the incidents in Inaba that took place the year before. After giving his report to Mitsuru, he decides to return to his post, leaving Naoto behind to tail Mitsuru and the others.
Why do I believe it's Kurosawa? There are 3 things that we know so far about the person behind this "eerie voice:" It knows about personas/personae and shadows, It does NOT have a persona and it's somehow connected to the Kirijo Group; Kurosawa fits that criteria. There is also the fact that Kurosawa happened to find Mitsuru's group on the same place where Labrys was thrown into the TV. How would have he know of that place? How would he have known that Misturu and the others were going to be there, unless he had already planned it out; the criminal always return to the site of the crime. Another fact that stacks against his is that he purposely led Naoto to follow Mitsuru into the TV. Why? Well, if you play the other characters' story, it will be revealed that the Malevolent Entity is trying to gather powerful Personas/Personae to turn them back into shadows. Naoto might have never entered the tournament if it wasn't for Kurosawa.
My accusation is only based on circumstantial evidence. There are others that might fit the bill, such as Ikutsuki as we never really see him die. It could have all been a coincidence, but after my experience with Persona 4, in where the criminal was right in your face and giving the player hints, it is safe to say that I might be close to the truth.
Please feel free to comment and check if I there is any mistakes in my statement, as well as posting your own ideas.