Thousands of Sydney train passengers have faced delays of up to three hours after the scheduled replacement of an old signalling box took longer than expected.

There are fears the delays could run on into the busy Monday morning commute, crippling Sydney's transport network.

Angry passengers took to social media on Sunday to vent their frustration, as services going through Sydney's Central station were either delayed or altered.

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Kris Cetinski posted on Facebook that she was more than two hours late for work after it took her four hours to travel from Seven Hills to Mascot.

"Hopefully Sydney Trains can lift their game so things like this stop happening," she wrote.

"I wonder what the chances are of [Sydney Trains] reimbursing me the hours of pay I missed?"

Other passengers reported delays of 45 minutes between stations, or trains that headed in one direction before being diverted back to a station it had already passed.

Many passengers also complained that transport apps did not keep them updated about the changes.

Replacement buses were running between Strathfield and Central, as well as between Central and the North Shore.

By afternoon, passengers queueing for buses at Strathfield station began chanting: "Where's our bus? Where's our bus?"

Passengers at Strathfield station wait for replacement buses. ( Facebook: Kris Cetinski )

Some passengers on Sunday morning found themselves stranded at Olympic Park when there were not enough buses to accommodate those who had been removed from the trains.

Chief executive of Sydney Trains, Howard Collins, estimated that "several dozen" trains were affected after the analogue Sydney signal box was disconnected and replaced with a digital system between 11:00pm Saturday and 6:00am Sunday.

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To make matters worse, scheduled trackwork had closed the City Circle line over the weekend.

"It took a longer time to get platforms one to 14 at Central Station back into service [this morning]" Mr Collins said.

"We eventually got those back at 9.30am and we're now obviously recovering the operation."

As most trains travelled through Central, the delay had affected trains to and from suburban stations and as far as Grafton and Melbourne, he said.

Mr Collins said the system update was one of the most complex pieces of engineering work to be undertaken on the rail network and involved moving the signalling operations to Homebush.

Some passengers were diverted to Olympic Park and told to catch buses. ( Twitter: K Scott Huntley )

"It's a case of you have to do this some time, you can't just magically switch from one side to the other," he said.

"If people could see the thousands of cables and wires that we were cutting over.

"This is almost like open-heart surgery and trying to make sure the patient is recovering well, and that's what we're doing."

Mr Collins said he expected most delays to have been cleared by Sunday afternoon and the main focus would shift to ensuring passengers experienced a smooth commute on Monday morning.

Responding to criticism that passengers were not kept informed of changes, Mr Collins said additional staff were deployed to affected stations and loud speaker announcements were made to keep passengers in the loop.

"It's obviously never perfect and we've learned from feedback we've had and the information we've seen through social media," he said.