Is it necessary for overseas visitors to show their passport upon checking in at accommodations?

According to the Ministry of Health, Labour and Welfare, "Since April 1, 2005, under the relevant laws and regulations, the Japanese Government is requiring 'foreign nationals who do not possess an address in Japan' to provide their nationality and passport number in addition to their name, address, and occupation, etc. and produce and make a copy of their passport upon checking in at lodgings."

If you require any further information, please contact the Ministry of Health, Labour and Welfare.

https://www.mhlw.go.jp/stf/seisakunitsuite/bunya/0000130600_00001.html