The COVID-19 pandemic has seen health and medical research promoted as countries establish resilient health systems and rapidly responsive prevention, detection, and treatment methods. However, the pandemic will probably negatively affect the capacity and outcomes of the health and medical research sector itself.Research Australia is a national alliance of health and medical research stakeholders. In May, 2020, all members on Research Australia's contact list were invited to participate in, and share with colleagues, a 10 min online survey. The questionnaire contained 52 questions about research and employment and perceptions of the effect of the pandemic on researchers' activities (Deakin Human Research Ethics Committee project number HEAG-H-71_2020). Data were analysed with the use of descriptive statistics and logistic regression.1212 members responded, with most of the responses from researchers in the university sector (79·4%), who are early in their career (41·7%), working full time (70·9%), and in permanent positions (38·1%; appendix). Overall, 79·6% of participants indicated that their research was affected by the pandemic, with a further 9·7% of participants indicating that it was likely to be affected in the future. Commonly identified issues with current research were regarding participant recruitment in trials (49·3%), an inability to do research remotely (51·2%), and interruptions to the provision of equipment, supplies, and materials (28·4%). Most respondents reported effects on higher degree research students and early career researchers in their teams. Overall, 69·4% expected their own research to be affected after 2020, with the most commonly anticipated effects identified as delays in achieving project milestones (88·7%), publications (80·9%), and new funding (63·1%); reductions in overall funding (63·1%); and staff losses (45·8%).Perceived new developments in response to the pandemic included improvements in collaboration within their own organisation (31·5%), their own organisation pivoting existing research (33·2%), and improvements in ethics committee procedures (30·0%).Respondents from the university sector were less likely to have received extra funding related to COVID-19 from their institution (odds ratio [OR] 0·32, 95% CI 0·20–0·53) and more likely to have noticed an effect on higher degree research students (OR 2·19, 1·61–2·99). Relative to clinical researchers, public health researchers were less likely (OR 0·76, 0·53–1·09) and basic science researchers more likely (OR 1·75, 1·18–2·60) to expect their research outcomes to be affected after 2020, including any effects on higher degree research students (public health OR 0·51, 0·36–0·73; basic science OR 3·09, 2·04–4·67). Relative to early career researchers, mid-career researchers, but not established researchers, were more likely to expect their research outcomes to be affected after 2020 (OR 1·73, 1·25–2·40).This first Australian national health and medical research sector survey has highlighted that without an injection of funds from the government, this pandemic will have substantial short-term and long-term repercussions on research outcomes. These include a lower capacity to generate new products for industry, health services, and the community, and ensuring a workforce capable of responding to future pandemics with innovation and agility.