According to the ABC, more than 90% of Department of Prime Minister and Cabinet (DPM&C) union members who took part in a vote have supported strike action.
The industrial action could range from work bans to 24-hour strikes.
Over a quarter of DPM&C employees were eligible to participate in the vote.
In a statement, the department said it was committed to offering the best possible deal for its workforce.
“We respect the right of staff to take protected industrial action and we hope to come to an agreement as soon as possible,” it said.
“Malcolm Turnbull is now facing industrial action including strikes in his own agency, in what's a clear sign that public sector bargaining remains a mess that the Government needs to fix,” Nadine Flood, Community and Public Sector Union (CPSU) secretary, told the ABC.
“We have seen a small shift from Government but to resolve this impasse they need to drop the attacks on rights and conditions.”
The ballot was held following the rejection of the department’s pay offer in October.
The current employment agreements for thousands of public servants expired on June 30 last year, although workers at some agencies recently agreed to new contracts.
Turnbull’s government has already lifted the maximum pay increase for Commonwealth agencies from 1.5% per year to 2%.
Malcolm Turnbull could see workers in his own department take industrial action as public servants and the Government continue to clash over pay and conditions.