After nearly 48 hours of rail turmoil in Sydney, the NSW government on Tuesday afternoon backed down in its fight with the Rail, Tram and Bus Union, withdrawing proceedings against it at the Fair Work Commission.

The about-face came after the union says it called to see a copy of the safety assessment used to justify shutting down the network on Monday morning, a decision that disrupted hundreds of thousands of commuters, before limited train services resumed on Tuesday.

RTBU Secretary Alex Claassens described the union's industrial position as "vindicated", and reiterated that the shuttering of the network was done by NSW transport officials.

"It was quite clearly a decision made by government and senior bureaucrats," Mr Claassens told reporters at Central Station.

"Disappointingly, the use of that action, further disrespecting the (union) members and the general public, really has to be questioned at some point."

With the stoush at the industrial umpire now finished, Mr Claassens said the challenge was to get the system "back up and running properly", and pointed to Monday for a possible resumption of regular services.

"We're fairly confident we can do that, even with our protected action in place, without us having to lift any of them," he said.

"The challenge though, in the next couple of days, is for us to be able to sit down with management and try and work out how we improve the situation over the next few days.

"The reason we're in this situation still remains, the NSW government is refusing to deliver an enterprise agreement that enshrines basic safety and employment conditions for rail workers and commuters."

Trains on Tuesday ran at 25 per cent capacity, with buses supplementing some services, and a similar level of service is expected on Wednesday.

In a bid to keep peace talks moving, the government is set to meet the union later this week to discuss the city's train fleet, wages and safety.

Earlier, after meeting union officials, Transport Minister David Elliott fronted the media saying senior lawyers had advised the government to withdraw from the FWC proceedings, which he described as "in the interest of not only transparency but also goodwill".

"I have agreed with the union today that we will start to commence rewriting the enterprise agreement that expired in May last year."

He called the withdrawal an "act of good faith" from the government to get train services back to normal, and shrugged off suggestions he knew about the shutdown before it happened, insisting he was asleep at the time the decision was made in the early hours of Monday.

"I don't expect them to send a car around at two o'clock in the morning and wake me up and tell me," he said.

Labor leader Chris Minns welcomed the backdown, but said it was still unknown why the network was shut down.

"(Mr Elliott's) got to have some candour with the people of NSW, explain what happened over the last 48 hours," he said.

The system shutdown blindsided about half a million commuters, with many left stranded across Sydney, Newcastle, the Central Coast, Blue Mountains and Illawarra.

The union at the time insisted limited industrial action planned for the day would not have affected safety and workers were ready to run the trains.

It has been at loggerheads with the government over a new enterprise agreement since 2021 over safety guarantees, hygiene and privatisation concerns that has resulted in two work stoppages since September.

Premier Dominic Perrottet called the stoppage part of a "concerted attack" on the government by the union and Labor.

AAP