Importance Public health depends on both medical treatment development and the public’s willing-ness to take such treatment. Objective To determine whether having experienced delayed localized hypersensitivity reactions to COVID-19 vaccines, i.e., “COVID arm” symptoms affect confidence in the safety of vaccination, willingness to take COVID-19 vaccines, and the acknowledgement of the importance of vaccination, and also confidence in science. Design We implemented a survey in February 2021 and March 2022 in Japan, before and after COVID-19 vaccines were administered to the public in Japan, and we used “COVID arm” symptoms, which are independent of one’s prior confidence in vaccination, as our instrument. Setting We conducted a panel survey on internet. Participants Out of the non-probability sample of 15,000 respondents in the first wave in February 2021, 9,668 responded to the second wave conducted in March 2022. Intervention We used “ COVID arm” symptoms as a natural experiment conditional on the back-ground characteristics of the respondents. Main Outcomes and Measures Main outcomes are whether having experienced “COVID arm” symptoms affected 1)confidence in the safety of vaccination; 2) willingness to take the next dose of COVID-19 vaccines, 3) acknowledgment of the importance of vaccination, and 4) confidence in science. Measures are marginal means of the probability of a positive reaction to each question. Results Experiencing “COVID arm” symptoms significantly lowered confidence in the safety of vaccination by 3.4 percentage points and the probability of taking a second and third dose of COVID-19 vaccine by 1.2 and 3.4 percentage points, respectively. Adverse impacts were observed regardless of prior confidence in vaccination. Experiencing such symptoms affected neither the acknowledged importance of vaccination nor confidence in science. Conclusions and relevance Updates to beliefs about side effects affected confidence in the safety of vaccination. Acknowledgment of vaccination importance and general confidence in science are likely to have factored in the uncertainty and to be tolerant of updates to one’s beliefs about side effects. Belief updates of specific treatments had asymmetric impacts on the treatment and medicine in general. Trial Registration The design of the survey was preregistered with the American Economic Association’s RCT Registry .