The Nakatomi Purification Prayer is most centrally associated with the great semiannual rites of purification in the Shinto tradition. It is recited at the Ōharae, the Great Purification ceremonies held twice a year, on the last day of the sixth month and the last day of the twelfth month. These rites, sometimes known by names such as Nagoshi no Ōharae or Minazuki no Ōharae for the mid-year observance, function as a collective spiritual cleansing, addressing the impurities believed to have accumulated over the course of daily life. In this sense, the prayer serves as a kind of liturgical axis around which the rhythm of purification in the ritual year turns.

Beyond these great mid-year and year-end observances, the Nakatomi Purification Prayer may also be employed on other significant ritual occasions. It can be included in ceremonies that mark important transitions or require heightened purity, such as weddings or ground-breaking rites for new buildings, and it may be invoked after periods of mourning. In these contexts, the prayer extends its role from a strictly calendrical function to a more situational one, accompanying moments when individuals or communities seek to restore harmony and spiritual clarity. Through such uses, the text of the prayer becomes not only a formal recitation, but also a vessel for reorienting human life toward a state of renewed purity.