The government has put aside $53.7 million for work in 2019-20 on its flagship infrastructure project SPIRE.
The remaining funding of the project - with the total project expected to cost at least $500 million - has not been disclosed with the government citing commercial reasons.
Meanwhile, the government is predicting key performance measures of health services will continue to fall.
SPIRE - which stands for Surgical Procedures, Interventional Radiology and Emergency centre - is an expansion of Canberra Hospital that was a key election promise in the 2016 election.
The government would need to spend at least $146 million in the subsequent three years from 2020-21 to complete the project, based on the initial budget.
A further $6.5 million not spent this financial year on the project has been brought forward to next year.
The government says it is currently the largest single infrastructure project in the territory.
The $54 million is the first major allocation of infrastructure funding for the project.
It comes as the emergency department wait times in ACT's public hospitals are expected to plummet even further.
Budget papers show the ACT Health Directorate has predicted just 33 per cent of urgent (category three) patients in ACT's emergency departments were seen on time this financial year.
In 2017-18, the figure was 37 and by far the worst in the country.
The percentage of cancer patients starting radiotherapy on time also remains below target this financial year.
Only 70 per cent of palliative treatments started within the recommended time of two weeks, while just 50 per cent of radical treatments started within the recommended four weeks, the papers predict.
Health Minister Meegan Fitzharris maintained the government was committed to improving wait times, saying the increase in presentations to emergency was behind the poor performance.
MORE BUDGET NEWS
The budget also includes about $70 million in capital works funding over four years to create a digital health record across all of ACT's public health services.
It would provide a single point of reference for patient clinical records, replacing current electronic and paper based systems.
The government last year announced $70 million in funding for an expansion of Centenary Hospital - the women and children's part of Canberra Hospital.
But that figure has now been reduced by more than $20 million.
About $4 million in funding allocated for 2018-2020 for acute aged care and cancer patients has been pushed forward to 2020-21.
Health is the largest single area of funding with 31 per cent of the budget allocated towards it, up on about 30 per cent last year.
Australian Medical Association ACT president Antonio Di Dio said more funding to run ACT's hospitals and reduce wait times was needed.
"Only last week, I spoke at a seminar with former ACT Chief Minister, Jon Stanhope, and former ACT Treasury official, Dr Khalid Ahmed, highlighting the funding challenges that ACT public hospitals face," he said.
"While it's true that we need to look at how we can do things better, it's also apparent that the ACT Government needs to likewise look at how they fund our public hospitals.
"New infrastructure, whether that be the SPIRE Centre or additional operating theatres at Calvary Public Hospital are vital, but so is sufficient funding to run the hospitals and reduce elective surgery and emergency department waiting times."
The Australian Nursing and Midwifery Federal ACT branch secretary Matthew Daniel welcomed the budget's measures to improve workplace safety.
"There is no secret the health system is facing a number of challenges, particularly issues with nursing and midwifery safety, workload and work/life," he said.
"The health services must ensure that all nursing and midwifery workers have secure jobs.
"The use of unnecessary temporary contracts, especially for early careers nurses and midwives must stop."
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