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Stark cultural differences have emerged as management struggles to integrate the two departments. Photo: Tamara Voninski

Public servants at the merged foreign affairs department are on a collision course with their bosses after left-leaning AusAID trade unionists crushed their conservative DFAT colleagues in an internal power struggle.

The electoral rout of the Department of Foreign Affairs and Trade officials sets up a clash with departmental bosses as the heavily unionised AusAIDers prepare to defend generous entitlements built up before their agency was abolished.

As the Community and Public Sector Union's national leaders called for the feud to be left in the past, one DFAT public servant fired a parting shot at the victorious AusAIDers, accusing them of issuing a ''hardline Bolshevik manifesto'' in their hour of triumph.

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Bad blood between the two groups has been simmering since the uneasy marriage of Foreign Affairs and overseas aid departments was announced last September.

Cultural differences have emerged starkly as management struggles to integrate the two departments.

In the ballot for a head of the merged department's CPSU ''section'', AusAID veteran Aileen Croghan easily brushed aside DFAT stalwart Christopher Lang 466 votes to 149 with ballots falling along departmental lines.

It was widely expected the more heavily unionised AusAID workers would dominate the vote, but now delegates from the scrapped agency face wage talks with management dominated by DFAT bosses.

In her victory email Ms Croghan hit back at claims that AusAID union delegates were too close to the left wing of the Labor Party. ''Suggestions circulated to members and the media prior to and during the election about a takeover or link to party politics in these decisions are simply untrue,'' the newly elected section secretary wrote.

But one DFAT insider said the basic distrust between the two camps was still there.

The foreign affairs official described Ms Croghan's email as a ''hardline Bolshevik manifesto''.

''They say one thing and do another so the hypocrisy is still there,'' the DFAT worker said.

Another foreign affairs official simply said; ''They broke it, they now own it''.

Mr Lang refused to speak publicly about his defeat and the CPSU leadership said Ms Croghan was not available for interview.

A key source of friction between the two departments has been the perception in DFAT that AusAID conditions, particularly on overseas postings, are more generous than those of their new colleagues. They are expected to be a sticking point in the enterprise bargaining talks.

DFAT's media operation failed to respond to questions before deadline on Tuesday.

CPSU deputy secretary Rupert Evans played down the rift between the factions, saying it was good to see so many union members voting.

''The key focus of CPSU members and delegates now is fighting to protect jobs and services and dealing with the Abbott government's highly aggressive bargaining framework,'' Mr Evans said.