It may take a day for it to get into the system, but three days is a little excessive.
I'd contact the shipper, maybe they transcribed the tracking number incorrectly.
Although I have received every package that I have sent to the USA via EMS from Japan, there are other instances where I had to wait a substantial period of time for EMS packages to arrive from the UK.
I would say it should appear after 3 days, at least as number registered and accepted.
Is it a parcel that a shop has sent to you (meaning you were given the number via e-mail), or is that something you've sent out yourself while in Japan (meaning you have the exact number at hand)?
If it's the former, e-mail to ask again or the correct number sent to you.
There are also many possible kinds of network interruptions that might delay the tracking data from being updated.
It has been 3 days since "shipped" but when I try to track it on Japan Post's website nothing comes up. Shouldn't it at least have a input for acceptance by the Japanese post office? You should be able to track it at least till it hits the outbound port leaving Japan.
Good luck :) I have had no problems with two or three packages I sent from Japan to NYC via EMS......three days usually.