Queensland Rail said 300 fewer services would operate on the state's southeast network in and around Brisbane from Tuesday, with the new timetable to be similar to a Saturday.
There would be 15-minute and 30-minute intervals between peak-hour services instead of trains running every six to 10 minutes, it said on Friday.
The agency said a maintenance backlog linked to industrial action had caused "a shortfall of train availability", prompting the service cutbacks.
"This maintenance backlog means there are not enough trains to meet the full timetable," it said in a statement, adding the new timetable would run until further notice.
Queensland Rail and unions have been locked in weeks-long talks over a new enterprise agreement, sparking the protected action.
Transport Minister Brent Mickelberg said commuters should prepare for scaled-back services.
"Trains will be more crowded. It will be slower as more people are required to move in and out of the trains," Mr Mickelberg told reporters.
Queensland Rail chief executive Kat Stapleton said the action would impact commuters trying to get "to school, work, appointments and the footy".
"We know our customers are frustrated. I am frustrated too," she said.
"We want the unions to come back to the table and seriously consider the fair and reasonable and enhanced offer that we have presented."
The Australian Manufacturing Workers Union said train users were paying the price for poor planning from Queensland Rail and the state government.
"The AMWU has made it clear for weeks that industrial action can be withdrawn if agreement is reached," a spokesperson said in a statement.
"The solution is there - Queensland Rail and the LNP government need to stop playing politics, take responsibility and come to the table."
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