Engineers of safety-critical systems have a duty to address ethical issues that may arise in the development, assessment, operation and maintenance of these systems. Dealing with ethical dilemmas during safety risk assessment is particularly challenging, especially when making and justifying decisions concerning risk acceptability. This is particularly complicated by organisational issues and contractual limits that do not necessarily align with the boundaries of ethical responsibility. In this paper, we explore some of these dilemmas and discuss the duties of engineers to identify, analyse and respond effectively to ethical concerns about safety risk decisions. We illustrate these through short case studies that highlight particular issues relating to the ethics of safety advice, safety and cost tradeoffs, novel technologies and institutional support.