V/Line train services gradually resumed from midday Thursday following a near 36-hour suspension of all rail lines due to the Telstra outage on Wednesday.

Travellers were met with a second morning of cancellations on Thursday to peak services on all lines - Ballarat, Bendigo, Geelong, Gippsland and Seymour.

V/Line chief executive officer William Tieppo said the situation arose after the failure of the digital radio system which train controllers use to communicate with rail crews following the nationwide Telstra outage.

The outage occurred at 4:30am on Wednesday morning, caused by malfunctioning nodes that managed time synchronisation within some of the network data centres.

By 4pm Wednesday afternoon Telstra said they had resolved the issue, but a secondary fault was identified impacting calls, including Triple Zero.

As of 1pm on Thursday, Telstra chief financial officer Michael Ackland said this issue remained ongoing and needed to be addressed in a different way to the first.

“Mobile networks are complex and we continue to work through further changes to ensure we have the most robust solution,” he said.

“Customers can feel confident in calling Triple Zero.

“We'll keep working with our customers until every remaining issue is resolved, and as they complete all restoration and verification activities.”

On Thursday a V/Line spokesperson said services gradually resumed from 12pm after extensive testing of radio communications overnight.

“Before resuming services, V/Line conducted its own testing and operational checks to ensure communications between network controllers and train crews were stable, continuous and reliable,” they said.

“These tests were successful and confirmed that critical communications systems are operating at the level required for the safe operation of trains across the network.”

The spokesperson said passengers were advised some service delays may still be experienced as the network returns to its normal timetable.

“Passengers are advised to continue to check the V/Line website and app for up-to-date information as services are progressively restored,” they said.

“We acknowledge this has been inconvenient to many people and thank passengers for their patience as we worked with Telstra and ARTC to safely restore services.”

Mr Tieppo said the regional Victorian train service found it difficult to source enough replacement buses due to the unexpected nature of the shutdown.

“A disruption of this scale has been unprecedented for us, organising a bus replacement program for a whole network that normally runs thousands of people a day would normally take months to plan,” he said.

"This is a disruption for our passengers and the Victorian community; we're apologetic for that for our own customers and our own passengers.

“We want to make sure this doesn't happen again."

Mr Tieppo said customers can apply for compensation via the V/Line website where it would be reviewed on a case-by-case basis.