The deal to subsidise employee parking in Canberra is expected to cost the department more than $14 million, with the federal government's National Capital Authority confirming on Thursday that defence would not get a bulk discount.

While thousands of public servants elsewhere in central Canberra are hit with $12 all-day parking fees, defence and military bosses have struck a deal that will see their workers pay $4-a-day at the giant car parks at Russell Offices and Anzac Park West.

But departmental secretary Dennis Richardson and the Chief of the Defence Force, Air Chief Marshall Mark Binskin, have warned the relief is just temporary and parking will be still be on a "first-come, first-served basis".

Top brass who enjoy allocated parking will also have to pay the $4 daily fee, but disabled parking will remain free-of-charge.

Would-be interlopers from other departments will be foiled by an online registration system allowing ADF and defence APS staffers to register their personal credit cards to a website set up to verify their details.

Parking machines at the defence car parks will then charge registered cards the subsidised rate.

The full annual cost of parking for defence public servants and uniformed personnel was estimated at $19 million, indicating the with the parking measures might cost defence about $12.5 million.

But a defence spokeswoman said the price tag would be between $5 million and $10 million. She also said it had not been decided how long the subsidies would last.

But an authority spokeswoman was emphatic that no bulk discounts were being offered, that the NCA expected to collect $12 each working day for each space at Russell and Anzac Park West, and that any subsidies that were being offered were a matter between defence and its employees.

Federal departments throughout the triangle are grappling with the problems thrown up by the government's decision to start charging, from October 1, for parking spaces that have been free for decades.

The Canberra Times revealed last week that the Department of Foreign Affairs and Trade will hold a ballot to distribute precious car spaces in and around its buildings when it loses exclusive access to its prime Barton car park as part of the new arrangements.

Announcing the defence move to staff, Mr Richardson and Marshall Binskin said some of their workers were facing a 5 per cent hit to their annual wage without the parking subsidy.

Mr Richardson had previously said the charges would disproportionately hit young staffers and women who had to use their cars to drop off children.

"The defence committee has decided to provide some temporary assistance to staff [both ADF and APS] who would be liable to pay the full daily parking rate, noting that for some staff the $12 per day would amount to a reduction in take-home pay of more than 5 per cent," the two bosses wrote.

"Staff should be aware that the cost of parking will increase over time beyond the $4 per day and, at some point, full payment will be introduced."