And an email sent by one of the rail operator's senior staff last month appears to show the company responding to the massive repair backlog by simply deleting reports of faults if they had not yet failed.

Public Transport Minister Jacinta Allan is preparing to offer Metro Trains another seven years running Melbourne's trains.

Metro has received government payments of around $6 billion since then premier John Brumby appointed it in 2009.

Its most recent financial return shows revenue of $1.28 billion last financial year, and a $57 million profit.

The train operator is a joint venture between the Hong Kong-based MTR Corporation (which owns 60 per cent), and two Australian engineering companies, John Holland Group and UGL Rail, which own 20 per cent each.

Ms Allan will begin the process to re-sign Metro Trains at the end of this month.

But the Rail, Tram and Bus Union has warned that Metro is not looking after the city's rails adequately.

It has asked Ms Allan to take the rail network back into public hands, or at the very least run a competitive tender in which other companies can bid against Metro.

A report by Metro staff, compiled by track inspectors in the middle of August, showed there were 5838 track faults on the network.

The faults ranged from the mundane – broken bolts, loose screws, cracked sleepers – to more serious matters such as deep mud holes or a pedestrian crossing that was a "hazard for wheelchairs and walking aides".

Scores of track faults were reported up to two years ago and remain broken.

Those included on the list and inspected by Fairfax Media on Tuesday included parts of Oakleigh station.

The leaked report notes that in August 2015 a site inspection revealed Metro staff concerns about "drainage around the subway roof on the up [city-bound] track where the rails are directly fixed to the concrete deck".

Train passengers using the subway on Tuesday morning had to find gaps in the dripping water to avoid getting wet. Some used their umbrellas to stay dry.

The report lists hundreds of rotting sleepers throughout the rail network that need replacing.

One fault report notes "44 sleepers in a row in poor condition need to be replaced ASAP" near Roxburgh Park station. The report was first made in September 2014.

On Tuesday, an inspection of the rail line in that section revealed timber tracks still broken and rotting, although they had been covered with fresh ballast.

A more recent report from July this year said the level crossing next to Glenhuntly railway station had "bitumen [that] has broken away around the rails ... exposing them, vehicles can possibly damage their wheels travelling over the crossing".

A visit to the site on Tuesday showed the crossing had not yet been repaired.

The level crossing next to Glenhuntly railway station, noted in Metro Trains' track fault report. Photo: Joe Armao

An email obtained by Fairfax Media that was sent on August 18 by one of Metro's track maintenance managers said that the operator had completed a "bulk close-out" of track faults.

This meant Metro would not be fixing these faults because, the email said, "it was reasonable to assume the vast majority of these old faults … should have been fixed or since failed in track due to the extensive time interval".

Metro spokeswoman Sammie Black said the email was "an internal and confidential communication" that was part of a review of track fault data that had "identified some administrative anomalies". It meant some older track faults were still being recorded as needing to be fixed but "had been fixed or superseded".

She said the rail company's maintenance program complied "with the standards expected of us", and that Metro was spending "more than $1 million each working day on maintenance and renewals".

"Our track inspection methods both with track inspectors as well as our mechanised track inspections ensure all faults are safely managed," Ms Black said.

"All issues are fixed within specified timeframes", or monitored until they could be fixed outside train running hours, she said.

The state secretary of the Rail, Tram and Bus Union, Luba Grigorovitch, said Metro was not providing the reliable railway it had promised when it was appointed to run Melbourne's trains. She argued the company only reacted to serious maintenance issues rather than the rigorous proactive regime it promised when it took over from Connex in 2009.

"We currently have hundreds of faults across the network that before privatisation would have been fixed within a week of being identified," she said, arguing Metro was cutting corners to improve its profitability. "The government and the public would be mortified if they knew how often these cost-cutting measures were occurring."

Metro's plan to gain control of Melbourne's rail network for another seven years is so well formed it has recently informed staff it has created a new company, Metro Trains Australia, to focus exclusively on "securing an extension to our contract to operate Melbourne's rail network". The bid will be run by Metro's Andrew Lezala.

The public transport minister, Ms Allan, said the government would continue to consider how the train network could be run more safely, frequently and reliably.