Police discovered five bodies at an apartment in Hitachi City some 100 kilometres north of Tokyo after the blaze was extinguished in the early hours today, Jiji Press reported.
A child found in critical condition later died in hospital.
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Local media said the children were aged between three and 11.
A man in his 30s told authorities he had started the fire, according to Jiji, citing unnamed police sources. He is believed to be the father of the five children.
A police spokesman was not immediately available for comment.