Health Minister Simon Corbell says the ACT is the only state or territory to have its health and hospital funding slashed in 2017-18 to below this year's figures in the federal budget.
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The ACT government says it will lose $600 million in health funding over 10 years from 2017-18, according to its own analysis, with the switch from the National Health Reform Agreement to population based funding.
"The ACT is the only jurisdiction forecast to have a reduction in funding between 2014-15 and 2017-18 and will lose more than $600 million", Mr Corbell said.
In 2014-15, the ACT received $304.6 million under the national health reform agreement, which increases until 2016-17, then drops down to $296.1 million in 2017-18 when the agreement ends, according to this year's budget papers.
In every other jurisdiction, funding in 2017-18 is at least more than this year's figures.
A spokesman for Mr Corbell said the government calculated the $600 million cut by projecting the funding drops for the first 10 years without the agreement using the two years after it ends that are laid out in the budget (2017-18 and 2018-19).
It then compared these to 6.5 per cent yearly increases in funding if the agreement were to continue.
The spokesman said the 6.5 per cent figure was a "conservative" estimation of population growth and inflation.
Mr Corbell has said the ACT's funding shortfall from what was expected under the previous National Health Reform Agreement would grow from $14 million in 2017-18 and $22 million in 2018-19 up to more than $100 million a year in 2025-26.
"This failure to properly fund their share of hospital and health services will only put further pressure on our health system, which will continue to experience growth over the coming years," Mr Corbell said.
Liberal Senator for the ACT Zed Seselja responded, attacking the ACT government's figures and accusing it of running a health system with the "worst outcomes in the country".
"ACT Labor ... are now seeking to shift blame for this shocking performance by manufacturing figures which bear no resemblance to the truth," he said.
"Overall health funding for ACT hospitals is increasing 6 per cent in 2015-16 and 7 per cent in 2016-17."
Senator Seselja said this was more than federal Labor had budgeted for when it was in power.
"This year alone in the ACT the Coalition government has given $34 million more to the ACT than was budgeted by the Rudd and Gillard government," Senator Seselja said.
Mr Corbell said he would fight for a better deal than the cuts laid out for 2017-18 and beyond.
Responding to the budget, Australian Medical Association president, Professor Brian Owler expressed disappointment there was no indication last year's "savage cuts to the public hospital system" would be restored.
He also warned of the danger of other cuts laid out in the budget, saying the freeze on Medicare rebates could become a "co-payment by stealth".
"If the rebates don't rise, those costs have to be passed on in out-of-pocket expenses - we will see less bulk-billing, and there is the possibility of seeing a co-payment by stealth as has been alluded to by some," he said.
Mr Corbell said the ACT was also set to lose Commonwealth dental funding and indigenous early childhood development funding.
