Border Force staff began a strike at midnight as part of industrial action to protect pay and conditions.
Community and Public Sector Union national secretary Nadine Flood said travellers will be disrupted.
"It has ended up falling on a very difficult day," she told Network Seven on Monday.
"We weren't in a position to change the date," she said.
About 5000 workers will take part in the CPSU's 24-hour strike across the nation's eight international airports, ports, mail and cargo centres.
Nadine Flood fsaid the government has yet to come to the table with a reasonable offer.
"Border Force workers still face cuts to their pay and working rights, as do Immigration staff.
"We gave government a chance to fix it since the last strikes and unfortunately they haven't come to the table yet," Ms Flood told ABC TV.
"What we're asking is them to take pay cuts off the table," she said.
Some staff were facing pay cuts up to $8,000 a year, she said.
"We want this sorted well before Christmas."
With the volcanic ash cloud continuing to surround Denpasar Airport, airlines have cancelled flights.
Passengers on Virgin, Jetstar and Garuda Airlines flights to and from Bali are facing significant delays.
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