ACT senator Zed Seselja says he was disappointed about the decision announced on Wednesday to move public servants out of Canberra.
Mr Seselja said he would continue to fight to keep public service jobs in the national capital after Barnaby Joyce, as Agriculture and Water Resources Minister, said jobs from research and development corporations would be relocated out of Canberra.
Unions have accused Mr Joyce, who spent Thursday awaiting a leadership ballot for the Nationals, of pork-barrelling.
His announcement came despite rural research and development corporations already paying expensive lease costs in the national capital.
In May 2015, when news of Mr Joyce's decentralisation intentions surfaced, Senator Seselja said, "I think Barnaby's a little bit out on his own here ... it's going to be hard to make a financial case for it".
After the announcement, Senator Seselja said the same rules that stopped the Immigration Department being shifted out of the Canberra suburb of Belconnen could not be used in this instance.
"As a result of my work with the Minister for Finance, last year a decision was taken to ensure that any ACT-based federal government department would need to undergo a local impact statement before moving," he said.
"We are the first government to take these local impacts into account.
"The announcement by [Mr Joyce] relates to independent bodies that are, unfortunately, not bound by the same policy, though it's important to note that each of these agencies will retain a presence in Canberra."
Mr Joyce's decision appeared to go against the Finance Department's Operation Tetris project, which aimed to consolidate vast swaths of empty office space leased by the Commonwealth.
The Commonwealth has 34,000 empty desks in more than 500 buildings across Australia, according to the latest government data.
The RDC announcement will see staff pulled away from desks in Canberra offices, which still have up to eight years to run on leases.
Despite this, Finance Minister Mathias Cormann said: "This announcement by my good friend and colleague [Mr Joyce] implements an election commitment.
"As with the implementation of all of our election commitments, this will be implemented in the most efficient and least-cost way possible."
The Rural Industries Research and Development Corporation will relocate 12 staff to Wagga Wagga, the Fisheries Research and Development Corporation will move four to six staff to Adelaide and the Grains Research and Development Corporation will relocate half of its 50 or so staff to Dubbo, Toowoomba, Adelaide and Northam in the next two years.
Meanwhile, the Community and Public Sector Union said the Coalition's $20 million of cuts to six national cultural institutions in Canberra over four years must be reversed.
The National Museum of Australia, National Portrait Gallery, Museum of Australian Democracy, National Film and Sound Archive, National Gallery of Australia and National Library confirmed they would need to find significant savings by job cuts and changes to operations.
CPSU deputy secretary Beth Vincent-Pietsch said the government's cuts were "nothing short of cultural vandalism".
"There's been a long-standing issue of underresourcing of these institutions, so it's little wonder that budget cuts on top of that will have a terrible impact," she said.
"Inadequate funding puts the long-term health of priceless cultural relics in jeopardy, and could limit public access to these collections, including for the thousands of school kids who visit the cultural institutions each year."
"The people who stand to lose their jobs because of this harsh and unnecessary decision are skilled and dedicated, and the loss of their specialist expertise is impossible to put a value on."