What was the point of the Mutos EMP during the Stone Age?

i think it was actually used for communication between members of the species. those pulses when it was in the cocoon was it trying find the female and godzilla was "listening" in on them. at least thats what i gather from what i remember from the movie

^Which is pretty well explained in the first act of the movie. A mating call seems most likely.

I doubt Godzilla would have really hunted them down if the EMPs did harm to him. What animal runs torward something that can ultimately weaken it?

Of course, in the end the real reason the EMP is there is to make it difficult for the military to battle them so we have scenes like the halo jump.

These 2 posts above mine.

I doubt its a mating call, EMP's are not soundwaves like they descrived the echolocalisation, my theory is that they are a biproduct of the radiation they absorb, an EMP can be caused by nuclear explosions so in my opinion the mutos can cause micro nuclear reactions as a way to realese ecces energy and this causes the EMP

Well, it's already been answered before I showed up.

A very interesting question! I have been led to believe that some or atleast one of the Godzilla books released prior to the 2014 movie stated that the MUTO's EMPs were used to prevent Godzilla and other members of his species from firing their atomic breath. Now, as you said, this may not be offical canon. If so, then I believe the MUTO's EMPs may indeed have been used as a way to prevent King Ghidorah's species from firing their gravity beams during an encounter. That is, if King Ghidorah's species existed as another kind of prehistoric kaiju at the same time as the MUTOs, which I believe as I explained in my post discussing King Ghidorah's origins.