"We're building layer upon layer," Asa Hutchinson, undersecretary for border and transportation security, said at a forum on border security.
Hutchinson said the system, known as US-VISIT, would be expanded from airports to the 50 busiest land ports by December.
US-VISIT checks the identities of foreign visitors with digital photographs and scanned fingerprints against terrorist watch-lists and other databases.
Hutchinson said the department must use new technologies like biometrics and radio frequency to secure borders.
On the recently passed intelligence bill, Hutchinson said the department would work with states on a provision requiring national standards for driver's licenses. Hutchinson also defended the department's Secure Flight passenger-screening system, saying it would reduce the percentage of secondary inspections at airports.