We performed optical spectroscopy and photometry of SN 2006gy at late time, ~400 days after the explosion, with the Subaru/FOCAS in a good seeing condition. We found that the SN faded by ~3 mag from ~200 to ~400 days after the explosion (i.e., by ~5 mag from peak to ~400 days) in R band. The overall light curve is marginally consistent with the 56Ni heating model, although the flattening around 200 days suggests the optical flux declined more steeply between ~200 and ~400 days. The late time spectrum was quite peculiar among all types of SNe. It showed many intermediate width (~2000 km/s FWHM) emission lines, e.g., [Fe II], [Ca II], and Ca II. The absence of the broad [O I] 6300, 6364 line and weakness of [Fe II] and [Ca II] lines compared with Ca II IR triplet would be explained by a moderately high electron density in the line emitting region. This high density assumption seems to be consistent with the large amount of ejecta and low expansion velocity of SN 2006gy. The H-alpha line luminosity was as small as ~1x10^39 erg/s, being comparable with those of normal Type II SNe at similar epochs. Our observation indicates that the strong CSM interaction had almost finished by ~400 days. If the late time optical flux is purely powered by radioactive decay, at least M_Ni ~ 3 M_sun should be produced at the SN explosion. In the late phase spectrum, there were several unusual emission lines at 7400--8800 AA and some of them might be due to Ti or Ni synthesized at the explosion. (abridged)
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