It denied requiring US diplomats to undergo such tests last week after US media indicated that some had objected to the procedure.
“Some Japanese reported to our embassy in China that they received anal swab tests, which caused great psychological pain,” Chief Cabinet Secretary Katsunobu Kato said.
He added that it was unknown how many Japanese people had undergone such checks.
He also mentioned that the tests are used on some of those who are quarantined or entering China, adding that their use “has not been verified anywhere else in the world.”
He said China had not yet replied to the request, which was made by the Japanese government via the embassy in Beijing.