Almost a quarter of the global burden of disease and mortalities is attributable to environmental causes, the magnitude of which is projected to increase in the near future. Evidence informed policies and interventions are a key element in the adaptation response for countries. However, in many low- and middle-income settings, there remains a large gap in the synthesis of evidence on climate-sensitive health outcomes. In India, now the worlds most populous country, little remains known about the impacts of climate change on various health outcomes. In light of Indias vulnerability to climate change, the growing population and the high burden of disease, it is imperative to understand the challenges faced in conducting environmental health research. In this study, we employed key informant interviews to understand the perceived research barriers amongst health professionals, including medical researchers, and professionals involved in environmental policies and planning in Puducherry, India. The findings were analysed using data driven qualitative thematic analysis to elaborate the major perceived barriers to conducting environmental health research. Challenges in data collection systems and accessing data was the major barrier along with the need for strengthening technical and methodological research capacity. Participants described working in the backdrop of insufficient prioritization and knowledge on the wide range of impacts of climate change on health, both in the policy context and amongst scientists, which was also perceived to be a challenge in conducting environmental health research. Finally, limited resources to conduct research and the tendency to focus on conventional climate related health outcomes were also seen as challenges to advancing research on this topic. In the context of the paucity of data on environmental health from India, despite recognised climate change related health vulnerabilities, these findings could contribute to the development and improvement of interventions conducive to a strong research environment.