An industrial campaign by Jetstar's check-in staff could force the airline to increase fares, the company says.

Staff at six Australian airports are waiving excess baggage fees today as part of their claim for a five per cent wage rise.

The action, dubbed a "no weigh day", will cost the airline AU$50,000, says Ingrid Stitt from the Australian Services Union (ASU).

It is the first industrial action to hit the airline since its launch in 2004.

"Our members have endorsed a range of industrial actions, and they don't do that lightly," she said.

Affected airports include Sydney, Melbourne, Avalon, Cairns, Brisbane and the Gold Coast.

Jetstar chief operating officer Mark Dal Pra says flights will not be affected, but further action could force an increase in fare prices.

"Longer term, those sorts of actions can inhibit our ability to offer low fares," Mr Dal Pra said.

"For now though, passengers aren't complaining."

The airline says passengers at affected airports should expect to pay full baggage fees because some check-in staff are not taking part in the action.