Stephen Harrison, director of policy, identity and the passport service, said biographical and biometric data would be stored on two separate IT systems to ensure maximum security.
He also said, "There needs to be further reassurance about transparency, accountability and how safeguards will be put into place," and added a strategic action plan was published in December last year.
With oversight from Parliament and a newly appointed identification commissioner, Harrison said the system will be "strong, and can be strengthened further".
Access and technical controls will also be in place on the databases, aiming to guard against internal misuse.
Harrison also spoke of tough penalties, with the maximum prison sentence for misusing the data being 10 years.
He was speaking at the seminar Big Brother Britain?: ID cards, Surveillance and Data Security, and attempted to reassure citizens that ID cards would not be used as a surveillance tool.
He said, "The card can only hold limited information. It does have some potential to be used for surveillance, but mobile phones and credit cards leave more of an electronic trail behind us than the cards ever will."
Benefits outweigh the surveillance aspects, he said, with increased access to public services, greater convenience at borders and lower levels of ID theft being the hoped-for advantages.
He added, "The National ID Scheme will make it much easier to control our borders, and detect people applying for multiple IDs." Only police and security agencies will have access to the data, he said.