Objectives Limited literature exists on the practice of clinical supervision (CS) of professional physiotherapists despite current Australian safety and quality health standards stating that CS is to be provided to all physiotherapists. The aim of the present study was to evaluate the effectiveness of CS of physiotherapists working in an Australian public health service. Methods CS was measured using the allied health-specific 26-item modified Manchester Clinical Supervision Scale (MCSS-26). Subscales of the MCSS-26 were summed for three domain scores (normative, restorative and formative) and a total score was calculated, which was compared with the reported threshold score of 73 for effective supervision. Sixty registered physiotherapists (response rate 92%), working for a large metropolitan public health service, with six different site locations, completed the survey. Results The mean (± s.d.) total MCSS-26 score was 71.0 ± 14.3 (95% confidence interval (CI) 67.4–74.6). Hospital site was the only variable that had a significant effect on total MCSS-26 score (P = 0.005); there was no effect for supervisor or supervisee experience, or hospital setting (acute vs subacute). Physiotherapists scored a significantly lower mean percentage MCSS-26 score on the normative domain compared with the restorative domain (mean difference 7.8%; 95% CI 2.9–12.7; P = 0.002) and the formative domain (mean difference 9.6%; 95% CI 6.3–13.0; P < 0.001). Of the two subscales that form the normative domain, ‘finding time’ had a significantly lower mean percentage MCSS-26 score than ‘importance/value of CS’ (mean difference 35.4%; 95% CI 31.3–39.4; P < 0.001). Conclusions Within this publicly funded physiotherapy department there was uncertainty about the effectiveness of CS, with more than half the physiotherapists rating their supervision as less than effective, suggesting there is opportunity for improvement in the practice of physiotherapy CS. Physiotherapists scored lowest in the normative domain, indicating that they found it difficult to find time for CS. What is known about the topic? Previous research into CS for allied health professionals has shown that, on average, it is effective. However, these results cannot be generalised to specific allied health disciplines. Currently, the effectiveness of CS for physiotherapists is unknown. What does this paper add? This study is the first to investigate the effectiveness of CS in a large physiotherapy department of a publicly funded Australian healthcare service. What are the implications for practitioners? Requiring all physiotherapists to receive CS may not be useful if supervision is not effective. Finding time for CS appears to be the main barrier to effective CS. Focus should be directed towards developing a framework within which to practice CS that includes protected time for participation in CS.