Introduction Efficient case reporting via the Integrated Disease Surveillance (IDS) system is one of the main strategies to control of Lassa fever. Diagnosing Lassa fever is complicated by similarity of case presentation with common environmental causes of fever like malaria and typhoid, and limited laboratory capacity for identification. Objectives This study was conducted to assess trainee doctors' capacity to recognise and IDS report Lassa as well as institutional mechanisms for IDS. Methods Mixed methods, questionnaire survey of 260 doctors and key informant interviews with record officials. Results Over 65% of respondents correctly identified case definition of Lassa fever and most evidenced positive attitudes towards requirement of reporting despite work and time constraints. Relevant knowledge for IDS reporting was however poor. Over 30% of respondents did not know they were obliged to report these cases to public health authorities. About 50% did not realise a single suspected case constituted an emergency worth reporting and only 12% knew which forms to use. None of the physicians who had patients with symptoms matching case definition reported these to the local PHC office. Prior knowledge of the IDS system was due mainly to undergraduate learning experience. The institutional reporting mechanism had lapses IDS manuals were not available in any of the clinical practice areas, reporting forms and posters of case definitions were absent and clinicians did not maintain registers of patient diagnosis. Conclusion Lassa fever is unlikely to be reported through the IDS system. Efforts should target improving institutional compliance with regulations and increased education targeting physicians.