BackgroundPractitioners’ perceptions of patients with obesity and obesity management shape their engagement in obesity care delivery. This study aims to describe practitioners’ perceptions, experiences and needs in managing patients with obesity, determine the extent of weight stigma among health practitioners, and identify the factors associated with negative judgment towards patients with obesity.MethodsA cross-sectional online survey was conducted from May to August 2022 with health practitioners commonly involved in obesity management in Peninsular Malaysia, including doctors in primary care, internal medicine and bariatric surgery, and allied health practitioners. The survey explored practitioners’ perceptions, barriers and needs in managing obesity, and evaluated weight stigma using the Universal Measures of Bias – Fat (UMB Fat) questionnaire. Multiple linear regression analysis was used to identify demographic and clinical-related factors associated with higher negative judgment towards patients with obesity.ResultsA total of 209 participants completed the survey (completion rate of 55.4%). The majority (n = 196, 94.3%) agreed that obesity is a chronic disease, perceived a responsibility to provide care (n = 176, 84.2%) and were motivated to help patients to lose weight (n = 160, 76.6%). However, only 22% (n = 46) thought their patients were motivated to lose weight. The most frequently reported barriers to obesity discussions were short consultation time, patients’ lack of motivation, and having other, more important, concerns to discuss. Practitioners needed support with access to multi-disciplinary care, advanced obesity training, financing, comprehensive obesity management guidelines and access to obesity medications. The mean (SD) of the UMB Fat summary score was 2.99 (0.87), with the mean (SD) domain scores ranging between 2.21 and 4.36 (1.06 to 1.45). No demographic and clinical-related factors were significantly associated with negative judgment from the multiple linear regression analyses.ConclusionPractitioners in this study considered obesity a chronic disease. While they had the motivation and capacity to engage in obesity management, physical and social opportunities were the reasons for not discussing obesity with their patients. Practitioners needed more support to enhance their capability and opportunity to engage with obesity management. Weight stigma in healthcare settings in Malaysia should be addressed, given the possibility of hindering weight discussions with patients.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12913-023-09759-z.