Vaccination policies have shifted dramatically during COVID-19 with the rapid emergence of population-wide vaccine mandates, domestic vaccine passports and differential restrictions based on vaccination status. While these policies have prompted ethical, scientific, practical, legal and political debate, there has been limited evaluation of their potential unintended consequences. Here, we outline a comprehensive set of hypotheses for why these policies may ultimately be counterproductive and harmful. Our framework considers four domains: (1) behavioural psychology, (2) politics and law, (3) socioeconomics, and (4) the integrity of science and public health. While current vaccines appear to have had a significant impact on decreasing COVID-19-related morbidity and mortality burdens, we argue that current mandatory vaccine policies are scientifically questionable and are likely to cause more societal harm than good. Restricting people's access to work, education, public transport and social life based on COVID-19 vaccination status impinges on human rights, promotes stigma and social polarisation, and adversely affects health and well-being. Current policies may lead to a widening of health and economic inequalities, detrimental long-term impacts on trust in government and scientific institutions, and reduce the uptake of future public health measures, including COVID-19 vaccines as well as routine immunisations. Mandating vaccination is one of the most powerful interventions in public health and should be used sparingly and carefully to uphold ethical norms and trust in institutions. We argue that current COVID-19 vaccine policies should be re-evaluated in light of the negative consequences that we outline. Leveraging empowering strategies based on trust and public consultation, and improving healthcare services and infrastructure, represent a more sustainable approach to optimising COVID-19 vaccination programmes and, more broadly, the health and well-being of the public.