The Nikkei rose 0.9 percent to 16,830.92 after earlier traversing positive and negative territory.
China stocks fell on Wednesday amid weak volumes as markets prepared for a long weekend holiday though investors are looking ahead to the possible announcement of mainland shares' inclusion in MSCI's emerging market indexes next week.
The blue-chip CSI300 index fell 0.4 percent, to 3,163.99, while the Shanghai Composite Index lost 0.3 percent, to 2,927.16 points.
Hong Kong shares were little changed on Wednesday and trading was tepid ahead of the Dragon Boat festival holiday.
The Hang Seng index fell 0.1 percent, to 21,297.88, while the China Enterprises Index gained 0.3 percent, to 9,027.82 points.
Reference: Reuters
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