AusAID staff have been warned to expect a "lengthy and complex process" as their abolished agency is swallowed up by Foreign Affairs and Trade.
But the body, which has more than 1400 Canberra-based employees, could give little detail to its workers on their future as the main public sector union voiced concerns about the jobs and entitlements of workers in AusAID and other scrapped agencies.
The Abbott government marked its first official day on the job on Wednesday by sacking three top public servants and abolishing two departments and AusAID, a stand-alone agency.
Another senior bureaucrat, Treasury chief Martin Parkinson, announced he had agreed to step down in mid-2014 and AusAID's director-general Peter Baxter went on "extended leave" just hours before his agency's axing was announced.
A statement from the office of Foreign Affairs Minister Julie Bishop denied that Mr Baxter had resigned as AusAID chief, but said that the government was looking forward to working with him in another senior role.
To add to the confusion on Thursday, DFAT secretary Peter Varghese paid tribute to Mr Baxter's service, adding that he was expected to "serve in a senior position elsewhere in government".
Mr Varghese issued a statement to DFAT and AusAID workers on Wednesday afternoon, warning they were embarking on a "major undertaking". "Clearly, this will be a major undertaking, both for the two agencies and for all our staff," he wrote.
"We are at the beginning of what will be a lengthy and complex process, which we will approach logically and strategically, in a considered and transparent way."
Mr Varghese said a "full-time taskforce", led by AusAID and DFAT veteran Jennifer Rawson, would begin tackling the problems thrown up by the forced merger.
At the Department of Regional Australia, Local Government and the Arts, which is being broken up and its functions transferred to various "gaining agencies", workers were told to carry on as normal until advised otherwise.
"Until further advice is provided, staff will continue to work from their current locations and on the current IT systems, phone numbers and mobile devices," departmental secretary Glenys Beauchamp wrote.
"For most of you, business will continue as usual in the short term, albeit with new reporting lines to the gaining departments."
Community and Public Sector Union national secretary Nadine Flood said the union was worried about the upheaval in the lives of public servants in the abolished departments and agency.
"Before the election Tony Abbott promised 'no shocks or surprises', but there are plenty of shocked and surprised people in Canberra and beyond today," Ms Flood said.
"There are concerns that some of these machinery of government changes may lead to further job losses.
"CPSU is seeking more details about how the changes will be rolled out to ensure our members' rights and entitlements are respected.
"Departmental mergers can be a very complex process."