Lost property contacts for JREast
http://www.jrpass.com/blogs/help-lost-property
Lost property contacts for Narita Airport
http://www.narita-airport.jp/en/trav...list.html#lost
Mentally think through your route from the last time you saw the phone to the first time you noticed it was missing. Are there places other than the airport, N'EX and railway stations that you might have left it? If so, it might have been handed into a police box near one of those locations.
Can you make a telephone call to your number?
Failing that, do you have any insurance policy for the trip? (or cover through a credit card etc.). If so, find out what you need to do to file a claim. (e.g. If you need a police document etc.)
Good luck. You couldn't have picked a better country to misplace something valuable ... so don't give up hope just yet.