One public sector agency chief has told his employees that a resolution to their workplace stand-off is now unlikely before late-2016 and a senior executive from a large agency says it was "desperate" for a settlement before an election campaign began.

As a result of the Prime Minister's announcement on Tuesday that he would seek a July 2 election, the Australian Public Service could be operating under caretaker provisions in just under three weeks.

That timetable would plunge many department bosses into the nightmare scenario of entering caretaker period with no enterprise agreement and with a workforce that has not had a pay rise since 2013.

Confusion reigns in the service about whether enterprise agreements under the Coalition's tough hardline bargaining policy can be finalised in caretaker mode with workplace deals usually requiring the signature of a minister.

But departmental leaders' problems are more than just procedural, with serious worries for their prospects of convincing workforces to accept tough new conditions with the possibility of a change of government just weeks away.

The exception is likely to be in the giant Defence Department which is expected to get a new agreement over the line when its 20,000 public servants go back to the ballots on April 28.

Departmental Secretary Dennis Richardson is taking no chances this time, organising roadshows at Defence sites around Australia to use his influence to try to reverse the knife-edge no-vote recorded last month.

A yes vote at Defence would be a much-needed boost to the Coalition's faltering public sector industrial relations strategy which has suffered a major reverse on military pay and conditions and only succeeded in convincing about 30,000 public servants, just one-in-five of the civilian workforce, to accept the new workplace conditions.

Large groups of public servants at the Department of Human Services, the Immigration department and the Australian Taxation Office, as well as numerous smaller departments and agencies, continue to resist the government's planned changes, rejecting enterprise agreements by large margins.

One departmental executive told The Canberra Times last month that he and his colleagues did not rate their chances of convincing their department's rank-and-file to accept the tough new conditions against a backdrop of a federal election and they were "desperate" to achieve a resolution before the campaign began.

One agency chief, Australian Nuclear Science and Technology Organisation chief executive Adi Paterson was frank in his assessment of the prospects of a pre-election settlement of his agency's dispute after ANSTO's workforce rejected a proposal last week.

"With a potential Federal election looming and Government caretaker provisions to come into play, the timeframe for bargaining and a new proposal to be drafted and presented to staff for voting is likely to be late in this calendar year," Mr Paterson wrote.

The position on finalising enterprise agreements during the caretaker period remains uncertain.

The Australian Public Service Commission did not respond on Tuesday to requests for information.

But the commission's latest public statement on the subject, in late March, was non-committal with the agency simply saying it would advise departments before caretaker protocols took effect.