Chaos on Sydney's train network caused by Wednesday's strike is expected to worsen on Thursday as a standoff continues between rail unions and the NSW government over a new pay deal.

Trains were delayed for up to five hours on some lines on Wednesday and rail authorities warned more than 1,000 train services could be canceled due to staff shortages to run trains as they watched the state transport agency introduce a series of work bans and strike action. Minister Jo Haylen said it had "killed" the network.

Wednesday's disruption was caused by a series of industrial action, but Sydney Trains bosses pointed to a union's refusal to carry out maintenance at Bondi and Homebush stations as the cause of some of the worst disruptions.

The Electrical Union (ETU) - one of the joint rail unions locked in talks - has again refused to carry out night maintenance at points - rail infrastructure that guides trains across different tracks.

The government said if the points were not certified as safe, the signal would revert to the default red position and trains would be unable to switch between tracks.

The signalman was then forced to manually move the trains through the red lights one by one, causing the trains to bunch up. Delays then flow through that line and the wider network.

This led authorities to warn that disruption would worsen on Wednesday night and Thursday. Residents are urged to postpone non-essential travel.

"Passengers will continue to experience long delays, service cancellations and significant service gaps on the rail network," Transport for NSW said on Wednesday.

T1 North Shore and Western Line, T2 Leppington and Inner West Line, T3 Liverpool and Inner West Line, T4 Eastern Suburbs and Illawarra Line, T8 Airport and Southern Line, Blue Mountains Line, South Coast and Central Delays on the Coastline and Newcastle lines are particularly severe, the agency said.

Another work ban includes certain train drivers operating 23km/h below the 80km/h speed limit.

Transport for NSW apologized to affected travelers, acknowledging that some trains on the T4 line were delayed for nearly five hours on Wednesday. More than 25% of services were canceled during Wednesday's morning rush hour.

Chaos throughout the morning resulted in long queues of people waiting to change buses, with commuters reportedly taking 40 minutes to travel between the two suburban stations and trains often being stuck on platforms due to a shortage of rail workers.

The unrest comes as the United Rail Union considers the state government's proposal to raise wages.

Eight months into negotiations on a new pay deal, with proceedings at the Fair Work Commission (FWC) and the Federal Court, Helen announced proposals for a 13 per cent pay rise, a 1 per cent efficiency improvement and a 1 per cent super pay rise over four years - well below the 32% of the railway union's combined demand within four years.

Helen said the preferential offer announced this week was made possible by an agreement to merge the two national agencies that operate Sydney Trains and regional trains over the next four years. The merger is expected to drive productivity gains and financial savings, including possible job cuts, to fund an additional 1% of growth.

Rail unions have until Thursday to consider the proposal, but NSW Rail, Tram and Bus Union secretary Toby Warnes said the union was lukewarm on the proposal.

Such a stance creates the prospect of continued strike action in the coming weeks, with the FWC only being asked to resolve the substantive disputes - wages and working conditions - in February.

In a statement, the RTBU called on the government to "stop playing politics" and "get back" to the negotiating table.

A spokesman said: "It is clear the government's strategy is to drag out this dispute for longer than necessary in order to influence public perception of the union."

Meanwhile, the NSW government said it may again seek legal action to undo the union's joint action.

"We are currently considering all legal options to ensure these conditions can be lifted and trains can resume running on time," acting NSW Premier Penny Sharpe said on Wednesday.

The RTBU said any legal action would only "waste tens of thousands of dollars" of taxpayers' money.

“The union will not accept any proposal to remove the safety provisions fought hard during the last Enterprise Agreement campaign as this would jeopardize safety and leave commuters with inferior trains and services.”