Labor's Katy Gallagher has accused her Liberal counterpart Zed Seselja of "betraying Canberra" after he voted to support a motion in the Senate endorsing the relocation of departments such as the Australian Pesticides and Veterinary Medicines Authority (APVMA) from Canberra to Armidale.

While the motion was defeated 29 votes to 28, Ms Gallagher said the government could reintroduce it to the Senate at a later date.

"The federal government is ignoring the fact that Canberra was established to be the location of public service, and now they can decide to start shifting agencies around and completely uprooting families and experienced staff," she said.

"We have major government departments here and that's fundamental to the [ACT] economy."

The APVMA was one of four government departments listed in the motion that will move from Canberra to regional areas, including the Grains Research and Development Corporation, Rural Industries Research and Development Corporation and the Fisheries Research and Development Corporation.

Planning is underway to relocate the Murray Darling Basin Authority from Canberra to regional offices in NSW, Victoria and Queensland.

Senator Seselja hit back at the claims of betrayal by voting to support the motion, saying he has kept several thousand public service jobs in the capital .

"I'll take my real wins for Canberra any day over Katy's grandstanding over a symbolic motion in the Senate," he said.

"The motion, regardless of whether it got up in the Senate, would have no bearing on the decision to move the APVMA, a decision I made my views clear on during the election campaign."

While the motion said the relocation of public service jobs from Canberra would result in "unprecedented engagement with farmers, growers...and the community in general", Senator Gallagher said further government departments could make a similar move interstate.

"Nobody is against creating jobs in regional communities, but it should be backed and be a good use of tax-payers' money," she said.