"We have lots of MTS files with Premiere Pro CS6. I can hear the audio just fine with VLC. If you drag it to the Premiere project it will miss the audio track. I have downloaded an updated version of Premiere Pro from Adobe. And still it won't handle .mts files?"
People who are start using an AVCHD camcorder like Sony NX70, Sony VG900, Panasonic SD90, Canon XA10, etc often have the same case- Adobe Premiere Pro not reading audio from .MTS file as quoted above.
Read related posts about the MTS to Premiere Pro issue, some guys recommend the Media Browser, so I tried that instead of dragging MTS files into Adobe Premiere. Unfortunately it still does not work. After speaking to an Adobe representative I was told this was because I don't have the entire AVCHD folder structure and metadata available, just the .MTS files, and that the reliable workaround to get the audio back into Premiere is to transcode MTS clips into another format like MPEG-2 that Premiere Pro can fully support. This will help you import the file correctly.