Abstract Background Physicians’ work with sickness certifications is an understudied field. Physicians’ experience of sickness certifying for longer periods than necessary has been previous reported. However, the extent and frequency of such sickness certification is largely unknown. The aims of this study were: a) to explore the frequency of sickness certifying for longer periods than necessary among physicians working in different clinical settings; b) to examine main reasons for issuing sickness certificates for longer periods than necessary; and c) to examine factors associated with unnecessary issued sickness certificates. Methods In 2008, all physicians living and working in Sweden (a total of 36,898) were sent an invitation to participate in a questionnaire study concerning their sick-listing practices. A total of 22,349 (60.6%) returned the questionnaire. In the current study, physicians reporting handling sickness certification consultations at least weekly were included in the analyses, a total of 12,348. Results The proportion of physicians reporting issuing sickness certificates for longer periods than actually necessary varied greatly between different types of clinics, with the highest frequency among those working at: occupational medicine, orthopedic, primary health care, and psychiatry clinics; and lowest among those working in: eye, dermatology, ear/nose/throat, oncology, surgery, and infection clinics. Logistic analyses showed that sickness certifying for longer periods than necessary due to limitations in the health care system was particularly common among physicians working at occupational medicine, orthopedic, and primary health care clinics. Sickness certifying for longer periods than necessary due to patient-related factors was much more common among physicians working at psychiatric clinics. In addition to differences between clinics, frequency of sickness certificates issued for longer periods than necessary varied by age, physicians’ experiences of different situations, and perceived problems. Conclusions This study showed that physicians issued sickness certificates for longer periods than actually necessary quite frequently at some types of clinics. Differences between clinics were to a large extent associated with frequency of problems, lack of time, delicate interactions with patients, and need for more competence.