Janne in Osaka first reported that the Galaxy Nexus was unavailable at several Docomo shops in his area. I've since also made the rounds. It's official - NTT Docomo is unable to guarantee whether new stock will ever become available. 入荷未定
Note that this phone is officially listed as "on sale" on the NTT Docomo product page. (発売中 in the above screenshot). While you can probably order/reserve one, it may be months (if ever) before it is delivered.
However, there are still handsets available. You'll just have to hunt for them. I've seen new and used ones at various shops in Akihabara, though some of the new ones were the SIM-free international version (for about ¥30,000). Buying the international version will require a Xi contract to use with Docomo.
There were reports back in December of supply issues in the US, so I guess this should be no real surprise. At least Docomo now knows the formula for a popular Android phone.