Evidence suggests that multiple factors affect implementation of school-based physical activity interventions. This survey study examined the factors that influence the provision of classroom-based physical activity to students in the early years of primary school in Australia. A social ecological approach guided questionnaire design and analysis. A 45-item online questionnaire was administered to Australian classroom teachers and assistant, deputy and school principals working with students in Prep/Kindergarten to Year 2. Descriptive analysis determined response frequencies and content analysis was used to identify common themes in open-ended responses. The survey response rate was 22%; 34 of the 75 participants answered at least 93% of the survey questions. Barriers to providing classroom-based physical activity include: insufficient time, limited training opportunities, limited resources, educator attitudes to physical activity, and confidence. Proposed strategies to overcome barriers include the provision of training and resources to improve educator knowledge of the benefits of classroom based physical activity for children’s health and learning, and to improve their confidence in delivering classroom-based physical activity. Creating a supportive school culture towards physical activity through implementation of whole-of-school physical activity policies is recommended. Overall, the results of this study suggest that multiple strategies, targeted at the individual (i.e., educator) and organisational (i.e., school) levels, may be necessary to enable Australian schools to overcome perceived barriers to providing physical activity opportunities to students in the early years of school during class time. Findings from this research elucidate how Australian schools may be best supported to implement classroom-based physical activity programs, as part of a whole-of-school approach to physical activity promotion.