An earlier plan to shut down the Opal card readers by Wednesday was dropped by the Rail, Tram and Bus Union (RTBU) over the weekend, following a government threat to launch court action over it.
The RTBU had planned to leave station gates open as it did last month, but to also deactivate the card readers, preventing commuters tapping on to pay for trips, as part of industrial action reported to cost the government more than $1 million a day.
The union is now confident it will prevail and have the readers switched off as part of its industrial campaign, calling the government's tactics "desperate".
The union withdrew its initial application to shutdown the readers, after the government appeared to identify a fault in its filing.
"We went through a fairly severe process to make sure that it was legal and above board," RTBU secretary Alex Claassens told media on Monday.
"However, the government of course, in its midnight application, identified that there may have been a particular issue with a process.
"So it was a matter of ticking boxes in a particular format."
A new application to switch off the readers was filed on Monday morning, which the union is confident will stand up, Mr Claassens said.
"It was just a last-minute desperate bid to try and stop us from locking those gates open and allowing the commuters of NSW to travel for free," Mr Claassens added.
He also said NSW Transport Minister David Elliott was "ranting" last week when he criticised the RTBU and claimed switching off the readers could be dangerous.
A decision over whether the Opal scanners can be shut down will be made during a hearing in the Fair Work Commission (FWC) in the next 48 hours.
If the commission accepts the actions, the readers will be switched off 10 days later.
The RTBU and the government met at the FWC on Monday for a second day of conciliation talks.
The two parties are locked in a long-running stalemate over the safety of a new intercity train fleet and wages and conditions for workers.
The government and the union need to find a way back to the negotiation table, NSW Labor Leader Chris Minns told media on Monday.
"We want to see an agreement between the two parties, we don't believe that the two sides are too far apart," Mr Minns said.
"It really comes to a small disagreement on one or two issues."
"I'd encourage both sides to get around the table, work towards a solution. I think everybody wants to see an industrial agreement here."
"Hopefully the two sides can get an agreement soon."
As part of its campaign, the union recently took Sydney Trains and NSW TrainLink to the FWC in a bid to keep negotiating a new enterprise agreement and changes to Korean-built trains that have been mothballed for years, with the union saying they are not safe to operate.
Premier Dominic Perrottet declared negotiations were over at the end of August and threatened to terminate the enterprise agreement if there was further industrial action, after weeks of union disruptions to train services.
Transport Minister David Elliott has been contacted for comment.
26°C