Striking a balance between the rapid availability of a novel vaccine while ensuring its safety, quality, and efficacy is a major challenge during a pandemic. We aimed to elucidate physicians’ attitudes regarding the novel vaccine during the influenza A/H1N1 pandemic of 2009, and to determine factors that affected their vaccination recommendations to patients.

Of a random sample of 1,000 general practitioners (GPs) in Japan, 515 participated in the cross-sectional anonymous survey conducted just before the novel vaccine was available (between 28 September and 18 October 2009).

A total of 453 GPs (88.3%) replied that they intended to receive the new vaccine themselves; however, only 177 GPs (34.6%) intended to proactively recommend it to their patients. The anticipated cost of the vaccine negatively influenced the intention to vaccinate themselves and their recommendations to patients ( P χ ² test). Results of multivariate logistic regression analysis showed that physicians with experience in influenza A/H1N1 patient contacts [1–20 contacts, odds ratio (OR) = 7.49 (95% confidence interval [CI]: 1.73–32.36), P = 0.007; >20 contacts, OR = 8.03 (95% CI: 1.77–36.50), P = 0.007, compared with no contacts] were more likely to recommend the vaccine to patients, whereas those with knowledge of the fear on the causal association between Guillain–Barré syndrome (GBS) cases and the 1976 swine flu vaccination in the USA were less likely to recommend the vaccine [OR = 0.66 (95% CI: 0.45–0.97), P = 0.036].

Results of our survey indicate that physicians experience a moral conflict regarding recommending the novel vaccine to patients, which may be the result of their own experience with the disease, knowledge of vaccine side-effects, and cost.