The incident was made public through questioning during a Public Accounts and Estimates Committee.

Gippsland South MP Danny O'Brien questioned Public Transport Minister Ben Carroll on the incident on behalf of Euroa MP Steph Ryan.

"Are you aware of an incident between two V/Line trains that occurred on a Melbourne-Seymour line on May 14?," he asked.

"I understand a V/Line train travelling from Melbourne to Seymour ran through two failed or extinguished signals and narrowly avoided a major head-on collision with a passenger train coming from Seymour."

Mr Carroll replied, "Yes, we are aware of that incident", and said "passengers are always told the truth" about the cause of delays.

"Every incident ... has to be investigated; we work very closely with our road safety partners," he said.

On May 14, V/Line reported on social media that "Seymour Line trains are currently experiencing significant delays due to a rail equipment fault".

Three services had already been cancelled before Colleen and Lyle Jackel arrived at Spencer Street station in Melbourne to catch the 12.05pm train to Wangaratta.

The couple were put onto buses when they reached Seymour.

"There were not enough seats for the people who were meant to go to Albury, so they came on our bus, and then they were off-loaded in Wangaratta," Mrs Jackel said.

"The ironic thing is, that day was the opening of the railway precinct at Wangaratta, and we're all rocking up in buses.

"The service is appalling - you can never be sure you will get a train."

It was 5.20pm when the couple got to Wangaratta.

Mr Jackel said while their service was not the one involved in a near miss, it was clear signal faults plagued the system that day.

"Obviously, some problem on the 14^th of May caused this," Mr Jackel said.

"Colleen emailed V/Line with a complaint and they blamed an animal strike in their response.

"The story changed from signal faults to animal strike.

"These things (faults) will happen on that antiquated system."

The double line block signalling that reportedly faulted has been used since the 1870s and is the last of its kind in Australia.

Mr Carroll indicated in the committee it would be upgraded but did not confirm details despite attempts by Mr O'Brien for clarification.

Shadow Minister for Regional Public Transport Steph Ryan said it was wrong to describe the section as "safe" and it had to be replaced.

"Two trains almost had a head on collision but the government didn't tell anyone about it," she said.

"The signalling system failed, endangering the lives of everyone on board."

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