The Government of Japan has conducted weekly national surveillance of notifiable infectious diseases for over 25 years. As of December 2025, 87 notifiable diseases are under surveillance, although the list has changed over time as new infections have emerged and others have been reclassified. Although weekly data are openly available, their formatting and preparation have been labour-intensive. An open-source R package, jpinfect, has the potential to improve data accessibility and analytical workflows for these datasets. In this study, we used the jpinfect package to summarize national surveillance data for 12 acari-borne diseases in Japan from week 14 of 1999 to week 52 of 2025, by prefecture and sex. In total, 18 295 acari-borne disease cases were reported nationwide. Eight diseases reported at least one case. Of these, scrub typhus (56.6%), Japanese spotted fever (32.9%) and severe fever with thrombocytopenia syndrome (6.7%) together accounted for more than 95% of all cases. Scrub typhus case numbers remained stable and widely distributed across the country, except for in the northern island of Hokkaido. Confirmed cases of the other two tick-borne diseases increased, notably in western Japan, but with new cases also reported in northern Japan. Lyme disease, relapsing fever and Q fever were sporadically reported at very low incidence levels (<0.2 per 100 000 population). In addition to providing an updated epidemiological overview of acari-borne diseases in Japan, this report highlights the potential of jpinfect to streamline the generation of national situation reports. The surveillance and analytical framework described here could serve as a model for other countries in the Western Pacific Region.