The union says the government is planning to fly hundreds of managers from interstate to act as "strike breakers" at airports.
"They're turning heavy-handed tactics on their own workforce, when sitting down and resolving this 18-month dispute would be a better option," union secretary Nadine Flood said on Sunday.
A department spokeswoman said staff were routinely deployed in different areas to meet operational requirements.
"The Department has in place contingency arrangements to protect Australia's borders and minimise impacts on the public and industry," she told AAP.
Border staff are voting on a proposed enterprise agreement, with the ballot closing on Monday.
AIRPORT STOPPAGES TODAY
* All times are in Australia time
• Sydney (7am-9am and 7pm-9pm)
• Melbourne Tullamarine (5am-7am and 9pm-11pm)
• Brisbane (7am-9am and 7pm-9pm)
• Gold Coast (6.40am-8.40am and 7pm-9pm)
• Cairns (4am-6am and 6pm-8pm)
• Adelaide (6.30am-8.30am and 8pm-10pm)
• Perth (5.30am-7.30am and 5pm-7pm)
• Darwin (4.30am-6.30am and 5pm-7pm)
- AAP