Government departments will have to buy-in to the ID card programme if they want to use the technology to cut fraud, or check eligibility for benefits.
The disclosure by the Home Office follows a statement by Home Office minister Andy Burnham that the government's £5.8bn cost projections for the project do not cover the costs of implementing the scheme across all government departments.
The figure only includes spending on the ID card project by the Home Office, the minister said.
"If government departments decided they want to make use of ID cards and the verification service, they would pay for that," a Home Office spokesman told Computer Weekly. "It will be a matter for each individual department to decide how to incorporate ID cards into their own systems."
The disclosure was seized on by opposition MPs. Mark Oaten, home affairs spokesman for the Liberal Democrats, said, "If the project were ever to get off the ground it would need the full co-operation of ministers for health, education, work and pensions and local government.
"The fact that the costs for those departments have not yet been factored into the headline figure suggests that people outside the Home Office are getting cold feet."
The statement comes in the wake of new costings by the London School of Economics, which estimate the total price of the scheme at between £15bn and £30bn.
A separate study by auditors KPMG for the Home Office has raised further questions over the total cost of the project.
The study, extracts of which were published by the government, warns that the "durability of the cards over the 10-year period is questionable," potentially adding to the cost of the scheme.
It also questions the government's assumption that biometric pods, used to take fingerprints, iris and facial images, would last five years.
"A five-year life for biometric pods, given their very heavy use and the rate of technology advance, appears to be optimistic," the report said.
The KPMG report reveals that the Home Office has yet to fully quantify the benefits of the ID card programme.
"The work will continue through to the end of the current phase and into the procurement and implementation phases of the scheme," it said.
Burnham said the KPMG report showed government assumptions on cost were accurate.