Union officials and train network representatives met in court on Saturday, as the NSW government continued urgent legal action to try and cull "go-slows" that crippled the train system a day earlier.
A staggering 95.3 per cent of all Friday's services were either delayed or cancelled, which Transport for NSW put down to 862 train drivers and guards not reporting for their normal shifts.
The operators said the network was running close to timetable with minimal delays, and only 16 cancellations by 9.30am.
"Passengers should continue to plan ahead and allow extra travel time as there may be some delays and cancellations across the rail network today, due to ongoing industrial action," they said in a statement.
At the Fair Work Commission, the government is pushing to stop what it has labelled "industrial sabotage", asking the court to stop what it says is unprotected action.
On Friday, Treasurer Daniel Mookhey described the flood of absences as a "sneak strike" and denied accusations of a lockout.
But Rail Tram and Bus Union officials denied exerting control over the major spike in drivers calling in sick.
RTBU divisional secretary Farren Campbell said the allegation they had organised a "sick-out" was an unfounded government narrative.
"That's absolute rubbish. What we saw yesterday is very squarely a result of the lockout notices issued by Sydney and NSW trains," he said.
"The beauty of the commission is what they actually do is examine facts, instead of running off with rhetoric and lies like you've seen in the media in the last couple of days."
Train officials have denied the union's claim workers had been locked out.
Further efforts to halt work bans will go before the commission's full bench on Wednesday.
The pay dispute has rumbled on for 10 months.
Union officials initially pushed for a 32 per cent pay rise across four years, but the government offered 15 per cent for the same period including a federally mandated superannuation increase.
The union later provided a counter-offer of about 20 per cent across three years, which it rescinded after legal action was launched.
The rail network typically transports about one million people a day who have faced repeated disruptions as negotiations have dragged on.
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