Airports and seaports around Australia could effectively close next month as the Commonwealth public servant pay dispute with the federal government continues to worsen.

Industrial action by Immigration, Customs and Quarantine officers over stalled negotiations on new enterprise agreements is set to impact on Australia's borders during July, the workers' main representative, the Community and Public Sector Union (CPSU) has warned.

Three out of four Department of Agriculture Forestry and Fisheries (DAFF) staff voted last week to reject management's latest wage offer. DAFF staff will shortly vote on protected industrial action after a legal challenge by DAFF failed in Fair Work Australia.

The CPSU will today apply for similar Protected Action Ballots for staff in Customs and Immigration (DIAC) who are also expected to reject their proposed agreements.

CPSU National Secretary Nadine Flood said these disputes have arisen because management in the three agencies are "refusing to consider a range of sensible compromises needed to make agreements acceptable to a majority of staff."

"Over 75% of DAFF staff have voted no to their agreement, making this one of the highest rejections we've seen by staff in the public service in recent years. Staff in DAFF have comprehensively rejected management's proposed agreement and are determined to fight for a better deal," Ms Flood said.

"They deserve an agreement that properly recognises the unpaid work they perform during quarantine emergencies, that protects their current conditions and delivers a pay raise that keeps pace with the rising cost of living.

Ms Flood said Customs staff are concerned that their new agreement fails to properly recognise the growing work demands on them including increased extra marine patrols and difficult shiftwork arrangements as Australian airports move towards 24-hour operations. Staff also have major issues around superannuation and the lack of back pay in the proposed agreement.

Meanwhile DIAC members, who are paid significantly less than staff in Customs and DAFF, are angry that their new agreement does nothing to address this long-standing pay inequity. They are also concerned at proposed cuts to existing conditions.

"Staff across all these agencies don't want to inconvenience the public, but if the agreements they are being offered aren't improved, we have no choice but to move towards taking industrial action," Ms Flood said.

"We'd prefer to resolve these issues without taking action, but the ball is now in the employers' court. We remain willing to meet at any time to seek a solution.

"Staff in each of the agencies do essential, challenging and often dangerous work. They deserve better deals than the penny-pinching, mish-mash of cuts on offer in these three substandard agreements.

" DAFF, Customs and Immigration management and the Australian Public Service Commission are hiding behind each other, while these agencies fail to resolve staff's concerns.

"Agreements that fail to recognise staff concerns will lead to a loss of morale in agencies that are already over-stretched," said Ms Flood.

Customs employs over 5700 staff across Australia and are responsible for a broad range of border security issues including; preventing importation of illegal goods, preventing illegal foreign fishing in Australian waters and people-smuggling. Industrial action by Customs officers could impact airports, cargo terminals, sea ports, mail centres and other services.

DAFF employs around 4000 staff across Australia, including quarantine officers and export meat inspectors. Industrial action could affect export quarantine inspections including meat, international air passenger quarantine inspections and other services.

DIAC employs about 7000 staff across Australia and around 1000 overseas. Industrial action by DIAC staff could affect the administration of travel visas, international airports, detention centres, asylum-seeker processing and other services.