In a globalized world, the frequency of transboundary livestock infectious diseases is increasing, and strengthening of farm biosecurity is vital to stabilize food production. The aim of this study was to understand the decision-making process for farm biosecurity among Japanese livestock farmers. Postal surveys using structured questionnaires were conducted on beef, dairy, pig, and layer farms in Hokkaido and Saitama Prefectures, which represent the principal production area and peri-urban Tokyo, respectively, as well as randomly selected broiler farms across Japan. The question items included the attributes of farms and owners, disease experiences, related associations and sources of hygiene information, attitude toward hygiene management, and compliance with the Standards of Rearing Hygiene Management (SRHM). The compliance rates were compared between livestock sectors. Univariable analyses were conducted using combined data from both prefectures, with the compliance rate as the outcome variable and the questionnaire items as explanatory variables, in generalized linear models. Exploratory factor analyses were conducted using the variables with
p
< 0.2 in the univariable analyses. The factors identified were classified into knowledge, attitude, capacity, practice, and structural equation modeling (SEM) was performed. The questionnaires were completed and returned by 97 and 66 beef cattle, 86 and 136 dairy, 67 and 45 pig, 20 and 39 layer farmers in Hokkaido and Saitama Prefectures, respectively, and 95 broiler farms. The compliance rate was significantly higher among broiler farms (88.9%) compared with the other sectors, followed by pig (77.1%), layer (67.2%), dairy (63.8%), and beef (59.1%) farms in Hokkaido Prefecture, and layer (64.9%), pig (60.0%), dairy (58.5%), and beef (57.6%) farms in Saitama Prefecture. Based on SEM, the decision-making process from greater knowledge to higher attitude, and from higher attitude to greater compliance with the SRHM were significant (
p
< 0.01) in all sectors. Higher capacity was significantly associated with higher knowledge in dairy, pig,break and layer farms (
p
< 0.01), and with higher compliance in beef, pig, and layer farms (
p
< 0.05). These results suggest that the provision of targeted hygiene knowledge to livestock farmers and the support to smallholder farms would improve biosecurity through elevated attitudes and self-efficacy.