Trains on five lines in Melbourne’s north and west run through North Melbourne to access the city, meaning the fault paralysed a large swath of the network while Metro crews worked frantically to fix it.

The fault was first reported about 5.21am.

The Upfield line, which runs from Upfield through Coburg and Brunswick, was the worst hit, with services completely suspended from Coburg. Buses were called in to ferry stranded passengers into the city.

Passengers on the Craigieburn, Sunbury and Williamstown lines all experienced delays of about 10 minutes into the city.

On the Werribee line, passengers travelling through the Altona loop endured long delays with trains replaced by buses. For those travelling city-bound from Werribee, trains ran directly from Werribee to Newport, where passengers needed to get off and change onto the Williamstown train to get to the city.

The fault comes just after Metro implemented its new train timetable, adding to the sense of chaos and frustration for commuters still adjusting to the new schedule.

Initially Metro warned the signal fault was not likely to be fixed before the morning peak, but the problem was fixed just before 7am and delays slowly began to clear.

By 10am, all services were operating normally, Metro spokeswoman Larisa Tait said.