Birth Defects (BDs) are a significant contributor to childhood mortality worldwide, yet BD surveillance and management in Low and Middle-Income Countries (LMICs) like India remain under-prioritised. This article presents findings from a population-based BD surveillance conducted in the Palghar district, Maharashtra, India, aimed at identifying challenges and solutions in the implementation of BD surveillance. The data on BDs was collected between April 2021 and March 2023 from 38 Primary Health Centres (PHCs), nine Rural Hospitals (RH) and three Sub-district Hospitals (SDH) from seven tribal blocks of Palghar district. A total of 402 BDs were identified during the study period through facility and community-based approaches. Certain challenges were encountered at different levels of surveillance including underreporting by healthcare workers (ASHAs), non-functional District Early Intervention Centres (DEICs), a non-operational web portal for data entry and parenteral barriers attributing to screening, referral and management of BDs. Measures were taken to overcome these challenges comprising refresher training for ASHAs, the creation of communication channels and the distribution of educational materials. These initiatives encouraged and significantly improved the reporting of Visible BDs (VBDs) through ASHAs and programs (Rashtriya Bal Swasthya Karyakram) at the end of the reporting period. This study highlights that addressing these system shortcomings could be effectively achieved through intersectoral coordination and the involvement of Health Care Workers (HCWs) aligning with programme objectives. It further underscores the need for improved infrastructure and training to enhance BD surveillance effectiveness in South Asian countries, especially in tribal regions.