He called for the government to reassure the public by commissioning and publishing a privacy impact assessment of the programme and granting stronger powers to the information commissioner to police the scheme.
Despite the government's attempts to clarify the purpose of ID cards, there were still many unknowns, making it difficult to assess whether the measures taken to secure data were proportionate, said Thomas.
"The technology is still at a fairly early stage. Most trials have been limited to a small-scale population. Moving to the full population raises questions. We cannot get this wrong," he said.
It was not clear whether police will be given the rights to access the data trails, retained to tackle organised crime and prevent terrorism, to investigate a wide range of other crimes. "Will they have access to the database for murder, rape cases or unpaid parking fines? Where do you draw the line?" he said.
Thomas said his concerns that the scope of the scheme could be extended over time had not been addressed.