CSIRO's new chief executive Larry Marshall could soon be faced with industrial action within his workforce.
On Friday morning the Fair Work Commission granted permission for the Community and Public Sector Union to run a ballot of its members in the science agency to gauge support for industrial action.
The ballot was expected to start in late March meaning industrial action could be launched by late April, a few weeks before the federal budget.
Already union members at the departments of Human Services, Veterans' Affairs, Agriculture and Employment and at the Australian Taxation Office were either taking or planning industrial action.
CSIRO Staff Association secretary Sam Popovski said negotiations over the new enterprise bargaining agreement had effectively stalled.
"The major stumbling block is CSIRO management's support for the federal government's unworkable bargaining policy, which mandates cuts to working conditions, rights and pay," Mr Popovski said.
"CSIRO staff are frustrated and dismayed by management's decision to target their workplace rights and conditions, especially following the brutal cuts to jobs and research."
CSIRO has been downsizing its operations following a federal government budget cut of $115 million and hundreds of job cuts.
"It is estimated that CSIRO will shed almost 1,300 jobs in a two year period, representing a 20 per cent cut to the workforce," he said.