Thousands of passengers in Melbourne‘s northeast will face lengthy delays on their daily commutes until at least next week as engineers work to repair damage caused during a train derailment.

Both the Mernda and Hurstbridge lines, which service 110,000 people on a daily basis, will remain suspended until next Monday after a train came off the tracks at Clifton Hill on Sunday night.

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Metro Trains chief executive officer Raymond O’Flaherty said it was too early to say exactly what caused the train to derail.

“We’re confident that we’ll resume passenger services on Monday morning, next Monday,” he said.

“‘This network is safe, I stand by Metro’s strong safety record over the last 15 years.”

The impacted carriage was only lifted from the tracks on Tuesday.

Passengers have been forced to use replacement buses resulting in delays of up to 45 minutes.

“I usually wait like seven minutes for the train, but now it’s like a long wait in the cold, it’s terrible,” one passenger told 7NEWS.

The derailment happened on what has been described as one of the tightest corners of the train network at Clifton Hill.

Around 55 passengers were on board at the time and no injuries were reported.

“That part of the rail network was originally built in the 1880s and the alignment of the tracks has not really changed significantly since then so the infrastructure could well be a factor,” Daniel Bowen, member of the Public Transport Users Association, said.

Hurstbridge Line passengers will need to use buses between Eltham and Parliament stations, while those on the Mernda Line will use buses between Reservoir and Parliament.

“We ask passengers to check station platform displays, listen for announcements, and allow extra time for their journey,” the Department of Transport and Planning said.

Works that were already planned as part of Victoria’s Big Build mean that buses will replace trains on the Hurstbridge Line between Heidelberg and Eltham until July 24.

Over 100 major road and rail projects are being developed through the Big Build, including the Metro Tunnel.