Internal documents have shown some ACT Health staff are likely to face high anxiety in the lead-up to the split of the organisation, while the structures of the new organisations are still yet to be finalised.
It comes after the government on Monday announced the two bosses of the new organisations.
ACT Health will split on October 1, with ACT Health overseeing governance and Health Services overseeing the delivery of clinical services.
The Canberra Liberals claim briefings obtained under freedom of information show key decisions around finance, logistics, reporting and staff arrangements will not be finalised until days before the split.
But Minister for Health Meegan Fitzharris said that was when parts of the project were due to be completed, and did not relate to decisions.
A briefing for Ms Fitzharris created by interim ACT Health director general Michael De'Ath, dated July 25, said some staff would likely be facing signifcant anxiety around the restructure.
"Anxiety surrounding the reassignment and appointment processes is likely to be high, particularly for staff whose units may be reallocated across the two organisations, are in non-ongoing positions, are on temporary transfer or occupy positions with higher duty allowance," the briefing said.
"Mitigation strategies for these groups will be developed once the structure has been finalised and the impact for different groups and individuals can be assessed."
The briefing said some staff were likely to lose salary packaging benefits due to the organisational change.
Opposition health spokeswoman Vicki Dunne said the documents showed the split was "policy on the run".
“Critical decisions on finance, logistics and staffing arrangements won’t be finalised until the eleventh hour, and in the meantime staff are being left in limbo," she said.
“They have every right to feel anxious about that.
“The shambolic process revealed in these documents leaves little hope that these pressing issues will be addressed as a result of the split.
“Labor is hurrying through massive changes to a core area of public service without having taken necessary steps and measures to explore all options and mitigate damage."
A spokeswoman for Ms Fitzharris said the transition was happening through a staged and planned process.
She said the proposed structures would soon be presented to staff for consultation and was confident the split would run smoothly.
"Once this is finalised, there is further work with staff that will continue up until and after the separation occurs," the spokeswoman said.
"This change is an essential evolution for our growing population and expanding health system, and will bring greater clarity about the distinct roles and responsibilities of frontline and corporate staff.
"This lack of clarity was highlighted by the initial accreditation report in March, which also noted the ACT is the only jurisdiction in Australia with a single departmental structure.
"Most importantly it will help us future-proof our health system so Canberrans know they can continue to access public healthcare where and when they need it.
"Since announcing on 23 March 2018 that ACT Health would become two new organisations, the minister has consistently said that staff and key stakeholders will have input into the design of the organisations. This co-design process is well advanced and will ensure the two organisations are set up for success."