The NSW government took the Rail, Tram and Bus Union to the Fair Work Commission after what it described as an "unprecedented" number of employees calling in sick on Friday.
A whopping 95.3 per cent of all Friday's services were either delayed or cancelled, which Transport for NSW put down to 862 train drivers and guards not reporting for their normal shifts.
But the commission dismissed the government's argument on Sunday, saying there was no pattern of co-ordinated action.
Sydney Trains CEO Matt Longland warned of "unpredictable delays and cancellations day by day" and urged commuters to plan ahead.
Frustrated interim Transport Minister John Graham urged train workers to cease their actions.
"Industrial action negotiation has been going on for 10 months. The government view is it's time to stop that industrial action (because of) the impact it's having on commuters and businesses," he told reporters on Sunday.
"This dispute over time has been about a range of things - at one point it was about running trains 24 hours a day, at another point it was about free fares, now it is about a $4500 sign-on bonus.
"We can't afford bells and whistles here."
The state opposition pounced on the fallout, saying the union's expected industrial action - along with the government's excessive threats to withdraw pay for sub-par shift performance - would inconvenience Sydney train commuters.
"What we're left with ... is that on Monday there's uncertainty," said the opposition's industrial relations spokesman Damien Tudehope.
"To both parties (the union and the government): are you in favour of the commuters of NSW or do you want to continue playing these games?"
The union's NSW secretary Toby Warnes said the government's losing track record at the commission indicates that workers have a right to be fairly compensated.
"This is really in the government's court to give commuters that certainty and not to use commuters as a football to further its industrial strategy," he said in a press conference on Sunday.
Mr Warnes said the government's dismissive tone would further put workers offside and they would not show up to work on Monday.
The end-of-year $4500 bonus has become a sticking point after the former coalition government agreed to pay it to the union in 2022 to end protracted industrial actions.
"There's no blank cheque. We can't sign a blank cheque to settle this dispute. If we did, there'd be another demand and in six months' time, we'd be back here again," said Mr Graham.
But Mr Warnes took aim at the government's characterisation of the union's bargaining tactics.
"This idea of us coming back with demands in six months is complete nonsense and I can tell people of NSW that we will not be coming back with new demands in six months," he said.
Union officials initially pushed for a 32 per cent pay rise across four years, but the government offered 15 per cent for the same period including a federally mandated superannuation increase.
The union later provided a counter-offer of about 20 per cent across three years, which it rescinded after legal action was launched.
The rail network typically transports about one million people a day, with commuters facing repeated disruptions as the 10-month long negotiations drag on.
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