An early example of haibutsu kishaku is the Mononobe clan's anti-Buddhist policies during the time of Buddhism's early introduction to Japan in the Kofun period. The Mononobe were opposed to the spread of Buddhism not on religious grounds, but rather because of nationalism and xenophobia. The Nakatomi clan, ancestors of the Fujiwara, were allies of the Mononobe in their opposition to Buddhism. Another example is the policies of temple closure and monk defrocking of the Okayama, Aizu, and Mito Domains, also adopted for political and economic, rather than religious, reasons during the early modern period. These domainal policies were in general based on Confucian anti-Buddhist thought. The Meiji period form of haibutsu kishaku, based on kokugaku and Shinto-centrism, was instead dictated by a desire to distinguish between foreign Buddhism and a purely Japanese Shinto.

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