Sydney Trains will consider reimbursing commuters on an individual basis after the system ground to a halt on Wednesday, leaving commuters stranded at peak-hour.
Trains stopped for an hour at 2:45pm after drivers lost contact on the digital radio system, which is used for emergency communication between train crews.
Some passengers were stuck mid-journey, left on the platform or directed to take buses or ride-share services.
Other passengers forked out to stay in Sydney for the night rather than wait for a bus or train.
"All of us apologise," Sydney Trains operations officer Howard Collins said on Thursday morning.
"There were journey times of two, three, four hours. Particularly for those on the Central Coast or in Kiama (two-hour drive south of Sydney)."
Look back at our live shutdown coverage
Mr Collins said they would consider reimbursing passengers on a case-by-case basis.
"Like all major incidents, we're quite happy to consider (reimbursing) individual cases if people think they have experienced hardship," he said.
"We'll listen and see what we can do to support them."
Premier Dominic Perrottet said he has asked the Transport Department to organise a day of free public transport to compensate for Wednesday’s shutdown.
"I've made it very clear to the secretary of the department that my expectation is there is a fare-free day to make up, some way, for what occurred yesterday," Mr Perrottet said.
A fare-free day would have to occur after the state election, given the government is currently in caretaker mode.
Sydney Trains chief executive officer Matt Longland said engineers worked overnight to detect the cause of the issue.
"We've done quite a bit of work to identify the root cause of the incident … we don't believe it was anything around cyber security," Mr Longland said.
"It's never happened before … we've never had an incident of this scale."
While Mr Collins said there was no indication "so far" of a cyber attack.
Mr Longland said a "component failure" occurred, which would usually automatically redirect the network to a backup system but, in this case, the backup system failed.
This meant engineers had to manually find the fault and fix it, before the trains could recommence.
Mr Longland said Sydney Trains had used a radio technology system supplied by Austrian company Frequentis, since 2016.
He said the network had been undergoing software upgrades over the last six months.
"That may have been a factor in this incident," Mr Longland said.
"We're monitoring it closely. Our engineers are on site and have been overnight to keep an eye on the system while we investigate over the next couple of days.
"We're working with (Frequentis) and our own people trying to get to the root cause of the issue."
He said the next steps would be to study the data logs and work out why the fault occurred, to ensure it would not happen again.
Trains were running to a normal timetable on Thursday morning, with "one or two" services delayed, according to Sydney Trains.
