The "Australian Border Force" could face a revolt in its ranks from Customs and Immigration officers being asked to cop big pay cuts when they join the new outfit.

Public servants set to transfer from Customs to join the Border Force are "going ballistic" over a move they say will leave them thousands of dollars worse off each year.

But the Immigration Department, which will merge with Customs in July, says it simply cannot afford to allow some conditions and entitlements to continue.

A Customs investigator battling organised crime will face a cut of more than $5800 a year under the new deal, according to their union the CPSU, while an Immigration officer managing the removal of criminals and deportees would lose out by $3000.

The public servants face the loss of a long list of the allowances that make up much of the take-home pay of officials in frontline roles in Immigration and Customs.

Union members at the two departments began to vote on Monday morning on potential strike action and their representatives are warning the mood has been ugly since the Immigration's Department's new bosses proposed stripping the allowances.

If no deal is struck before the July 1 deadline, all 13,500 workers in the merged department will go onto the existing Immigration deal, stripping Customs officers of many of their allowances.

The 3000-strong Australian Border Force, to begin operations on July 1, will exist as the "operational" arm of the enlarged department.

But CPSU national secretary Nadine Flood said the new force could be facing problems before it even begins operating.

"It's not an overstatement to say that Customs officers are going ballistic," Ms Flood said.

"They are absolutely furious that the combination of the government's draconian bargaining policy and the move to Border Force is being used to hang a threat over their heads and their take home pay could be being cut."

Ms Flood said the anger was palpable among frontline Customs officers in particular.

"Many of their reactions have been unprintable," she said.

"Our officials running meetings at the airport and mail centres in the past few days have heard some of the angriest, most visceral reaction we've heard anywhere [about the] Commonwealth government."

A departmental spokeswoman said the proposed pay deal had been developed in consultation with the Customs and Immigration workforces and was the best that was available under the financial circumstances.

"In developing this offer we have sought to provide the best possible outcome for our combined workforce in a challenging operational and fiscal environment," the spokeswoman said.

"While many employees would like to see the integrated portfolio adopt all of the most favourable conditions from the current Australian Customs and Border Protection Service  and Department of Immigration and Border Protection EAs, we are simply not in a position to do this as part of an affordable package."