The aim of this article is to identify a range of changes and challenges that present-day technologies often present to contemporary societies, particularly in the context of smart city logistics, especially during crises. For example, the long-term consequences of the COVID-19 pandemic, such as life losses, economic damages, and privacy and security violations, demonstrate the extent to which the existing designs and deployments of technological means are inadequate. The article proposes a privacy-preserving, decentralized, secure protocol to safeguard individual boundaries and supply governments and public health organizations with cost-effective information, particularly regarding vaccination. The contribution of this article is threefold: (i) conducting a systematic review of most of the privacy-preserving apps and their protocols created during pandemics, and we found that most apps pose security and privacy violations. (ii) Proposing an agent-based, decentralized private set intersection (PSI) protocol for securely sharing individual digital personal and health passport information. The proposed scheme is called secure mobile digital passport agent (SMDPA). (iii) Providing a simulation measurement of the proposed protocol to assess performance. The performance result proves that SMDPA is a practical solution and better than the proposed active data bundles using secure multi-party computation (ADB-SMC), as the average CPU load for SMDPA is approximately 775 milliseconds (ms) compared to about 900 ms for ADB-SMC.