A document released by the Office of the UK e-Envoy states: "The Government gateway has been designed to follow standards and allow people to use the computer system and browser of their choice."
The gateway is being developed by Microsoft.
Research by IT magazine Linuxuser revealed that Microsoft browsers and Windows machines enjoyed better access than other solutions.
The UK government confirms the problem is "with the way standards are implemented by vendors and a lack of offerings to manage digital certificates".
The government report adds: "Other browsers (running under Windows, Unix or Linux) can provide the required SSL connectivity but the ability to mange certificates on open source platforms needs investigating. The Office of the e-Envoy will be funding some activity by the open source community to address this issue."