Background Ambulatory care gives a better opportunity for medical students to acquire appropriate medical knowledge with diversity of cases. Identification and managing factors affecting clinical teaching of undergraduate students training in primary care will improve health out come in community. This study aims the identification of factors influencing clinical teaching hence to improve health care in outpatient. Methods A cross sectional study was conducted at College of Medicine and health Sciences. All students in clinical years invited to participates. Data was collected with self-filled questionnaire incorporating student’s perception regarding clinical teaching and learning. Data was analyzed using Statistical Package for Social Sciences (SPSS) version 20.0. Data was expressed in frequencies and percentages for questionnaire responses. Independent sample t-test was used to compare differences between two groups. Results A total of 100 students were participated in the study off which 62% were 6th year and 38% were 7th year students. Majority of students (99%) believed that lack of commitment to and interest in learning and increasing numbers of students in clinic influencing clinical teaching in primary health care. More than 40% of students believe that dedication and self-motivation in teachers is important factor along with inadequate supervision, teaching method, lack of feedback and conflicts between medical education and healthcare. More than half of the students think that inappropriate or small rooms for teaching, insufficient technological and audiovisual resources suitable for teaching and lack of institutional support are the main administrative problems. A significant statistical difference (p- 0.03; 95 % CI: -0.384-0.019) was observed between 6th year and 7th year students regarding student-related factors. However, no significant difference (p >0.05) was observed between 6th year and 7th year students regarding patients, clinical teacher and administrative support related factors. Conclusion Clinical practice is the most important component of health professional education. Undergraduate medical students require effective and conducive learning environment facilitates with appropriate supervision by teacher.