The NSW transport minister has apologised to Sydney commuters and admits the train network has been a "mess" over the past two days but says passengers won't be refunded.
The network went into meltdown on Tuesday afternoon leaving thousands of frustrated passengers stranded on platforms across the city, with rail bosses blaming lightning and driver sickness for the chaos.
Police officers were on hand to control the crowds while Sydney Trains suggested passengers use buses instead.
The network was initially affected on Monday by an increase in sick leave taken by train drivers and there were still delays on Wednesday morning with some services being cancelled.
But the Rail, Tram and Bus Union, the minister and Opposition Leader Luke Foley have all dismissed suggestions 70 drivers calling in sick on one day was linked to upcoming union pay negotiations.
"The chaos ... has absolutely nothing to do with the ballot we've been conducting with our members," a union spokeswoman told AAP on Wednesday.
"Sydney Trains and the NSW government really owe the public and their employees an apology for trying to blame workers for what's happened."
The union said suggesting a few people falling ill could cause a large number of services to be cancelled was "ridiculous".
Transport Minister Andrew Constance said the 48 hours of chaos was disappointing for commuters.
"I want to apologise," Mr Constance told reporters on Wednesday.
"We're not hiding from the fact that it was a mess. The trick is now getting it back on track as quickly as we can."
Despite being pressured by the Labor opposition, Mr Constance ruled out refunding train passenger fares for Monday and Tuesday.
"We need the funding for other services and to pay the staff," he said.
The minister wants the head of Sydney Trains, Howard Collins, and Transport Secretary Rodd Staples to report back to him within the next two weeks on how the network can better recover from major incidents.
Mr Collins says the new timetable introduced on November 26 will be reviewed but he insists it wasn't rolled out too early due to government pressure.
"My advice was that we were ready to operate the service at the end of November, I did say things would be tight," he told reporters.
Mr Collins admitted the more-intensive timetable meant when things went wrong it took longer for the system to recover.
He revealed Tuesday's meltdown occurred when the system was operating at just 50 per cent of its usual patronage.
The RTBU blames the new timetable for the delays.
"Management is scrambling to come up with daily excuses for the mess, but the reality is it's all to do with a poorly put together timetable," NSW secretary Alex Claassens said in a statement on Tuesday.
Mr Collins says he'll sit down with the union during the timetable review while Mr Constance has declared his door is "always open".
More train drivers are being recruited and by February the system should be "in a better position", Mr Collins said.
Mr Foley said the $2.5 billion set aside to rebuild three stadiums could be better spent on transport.
He wants the government to suspend the new timetable until more drivers and resources become available.