NeoGAF: Enterbrain numbers for June 12 to June 15 (4 days): 476,334
That number includes the regular edition, special edition, premium pack and the welcome box bundles. It is now the best selling PS3 game in Japan.
For reference, the first day numbers from Enterbrain not counting bundles was 300k (170k SE, 130k Regular). PS3 hardware for the week is 77,208 (Enterbrain numbers from the article as well).
For comparison, here are the first week figures for the MGS series in Japan, Enterbrain numbers:
MGS1 - 316,833
MGS2 - 456,747
MGS3 - 487,156