This paper presents a novel methodological framework to the definition of vulnerability indices in disaster risk management at container terminals, based on a top-down approach. This proposal is aimed at answering the need for improved consistency in information flows between implementors of risk management processes (e.g., terminal operators, port authorities, port risk committees) and risk analysts. It also answers to the risk assessment and risk management push from the latest risk management ISO 31000:2018 guidance to work toward a more integrated approach with upper level strategies. In order to better correlate the risk indices provided by risk analysts to operational and risk management objectives of risk-bearers, a method relying on a dynamic value-flow stakeholder analysis is carried out for the different phases of the risk management cycle. A methodology is presented in this paper to successively build the stakeholder model, characterise the performance targets and needs of each and hence the value flows that link them together. Once these are qualitatively assessed, a quantitative assessment of the value contribution factors of each stakeholder interdependency within the network is proposed, based on the model of stakeholders' satisfaction following a service-based operational approach. Once those key stakeholders' interdependencies are quantified and the critical stakeholders and links within the networks identified for the benefits of the container terminal operator, corresponding tangible vulnerability indices are defined. A dual approach to vulnerability indices definition is proposed. It consists in an internal operation vulnerability index and external contextual vulnerability indices that account for the environmental vulnerability contribution factors. The identification of the key internal operational vulnerability indices is based on fault tree analyses, whilst the contextual indices utilise the stakeholder model and existing macro socio-economic indices. Such vulnerability indices can then be utilised in natural disaster risk assessment frameworks consistently with key risk management decision making processes and corporate targets.