This could have probably been searched for, but I am feeling nice and will waste the bandwidth productively to answer you.
I assume Naruto 3 is an actual disk, and I assume for the purpose of this response that you are using a USB loader. I also assume you purchased the game online and had it imported. I know in USB Loader GX and in CFG USB Loader you can set the game options to force Pal. I am NTSC personally, so I do not know the difference between PAL 50 and PAL 60, but I suppose you might know the difference. If not, try one, then the other.