Sydney commuters will face further rail delays with trains operating at 60 per cent capacity for the rest of the week.

The NSW government made an application with the Fair Work Commission to halt further industrial action by the rail union which would see only 25 per cent of trains on the tracks operational.

While the industrial action scheduled for Wednesday will go ahead, Metropolitan Roads Minister Natalie Ward said the government had taken a "win".

"The Rail Trains and Bus Union (RTBU) has now lifted a range of industrial bans that will see 60 per cent of the train fleet operational by the end of the week," she said.

"This is a big step in the right direction for all rail commuters."

Ms Ward said the application didn't deal with all issues presented by the RTBU, and said a further three applications would be filed to the Fair Work Commission to suspend and terminate all planned action.

"We've seen quite a win in capacity for getting more trains back on the tracks.

"The last thing we need with the severe weather is people standing for more time on our platforms for 10, 20, 30 minutes trying to get where they need to go." 

Head of Transport for NSW Howard Collins said commuters should avoid rail travel due to the industrial action and heavy rain that has hit Sydney.

"Please don't make those non-essential journeys," he said.

"If you're travelling early tomorrow, check before you travel, make sure your time is running. And if you can delay your journey, particularly in the peak, where we expect will be under the most pressure." 

The RTBU said in a statement the Fair Work Commission decision was a "significant" win.

"The Fair Work Commission has today sided with the Rail, Tram and Bus Union and agreed it should continue the protected industrial action planned for the coming days. This is a significant win and we should take a moment and celebrate that," the union said in a statement.

"However, it’s not over yet ...We are going to fight it with everything we have."

Trains have been disrupted since late June as negotiations broke down between the government and the unions over the safety of the new intercity fleet.

The union claims the trains do not allow guards to properly view the platform before departing and want them modified before it will allow them to go into operation.

The state government said it was costing $30 million a month to store the trains and this week promised to spend $264 million to modify them in line with the union's demands.

A full hearing between the two parties will be held on Thursday.