Katherine Courtney, director of the ID card programme, said trials had shown that fingerprint, iris or facial recognition alone were not robust enough to accurately identify individuals, but could provide a solution if all three were combined.
"None of the most robust biometric technologies has been proven to do a one-to-many match on a database, at least not in the sort of timescale that would be effective for business use," Courtney said.
The pilot evidence would be used to tell ministers that "we cannot pick one, so we are going to have to look at recording all three", he added.
The development is likely to push up the cost and complexity of the ID card programme, already estimated to cost £3.1bn.
Courtney said, "We are fairly confident that by recording all three of these measures we will have a system that meets all functional uses."
Security experts have raised questions about whether separate biometric readings can be combined together effectively.
"It is all very well saying you are going to combine the three biometrics, but you could end up knowing less than with one biometric technology," said Richard Clayton, security specialist at the University of Cambridge.
"If you have three biometrics and two say no and one says yes, what do you conclude from that?" he said.
Courtney said the size of the proposed register - which will eventually hold "up to 100 million" records - meant there were no existing schemes from which developers of the ID card project could learn and that a large enough test model could not be created.
"It is not possible for us to build a test system at this scale without building the system," she said.
The Home Office was therefore proposing to build up the system "incrementally" with the flexibility to make changes to the design if necessary.