Background: The current study aimed to identify the perceptions and issues regarding the affordability, availability, and accessibility of COVID-19 vaccination and determine the extent of vaccine hesitancy among non-vaccinated individuals. Methods: A Prospective cross-sectional study was conducted among 575 individuals for a period of six months. All the relevant information was collected using the peer-validated survey questionnaire. An independent t-test was applied to check the association between variables. Results: Among 575 participants, 80.8% were vaccinated, and 19.2% were non-vaccinated. Among the vaccinated, 35.1% were vaccinated in private centres and 64.9% in public health centres (PHC). In total, 32% had accessibility issues and 24.5% had availability issues. However, responders vaccinated at PHC were having more issues in comparison to other groups which was statistically significant (p < 0.05). Among the 163 privately vaccinated participants, 69.9% found it completely affordable. Another 26.9% and 3.1% found vaccines partly affordable and a little unaffordable. Among the 110 non-vaccinated, 38.1% were found to be vaccine-hesitant. Conclusions: Individuals vaccinated at PHC experienced issues such as long waiting times, unavailability of doses, and registration. Further, a significant level of hesitancy towards COVID-19 vaccines was observed. The safety and efficacy of COVID-19 vaccines contributed to negative attitudes.