Thirteen Metro Trains staff have been sent home to self-isolate after coming into contact with a Flinders Street Station employee who tested positive for coronavirus.

In an internal email seen by The Age, Metro Trains chief operating officer Catherine Baxter told staff an investigation they conducted identified 13 people who had come into close contact with the individual.

Many public transport users were wearing protective face masks at Flinders Street Station on Sunday.CREDITENNY STEPHENS

"Through our investigation, it was established there were 13 employees from the station team who had come into contact with the unwell employee," the email said.

"Most of these were for a short period of time and therefore the risk of transmission would be low. These employees have been notified with instructions to self-isolate and seek a COVID-19 test."

Metro told workers that the individual did not perform any passenger-facing activities during this time and that after discovering the positive test, it locked down parts of Flinders Street Station to deep clean.

Last week, Metro Trains staff working at Flinders Street Station expressed anger after they were not told a contract cleaner had tested positive to coronavirus before they inadvertently found out a week later.

Cleaning company ISS informed its staff that a cleaner who regularly worked at Flinders Street had been at the railway station while infectious on Monday, June 15.

The cleaner was immediately sent home after feeling ill and later tested positive for coronavirus. Metro Trains did not tell its workers at the station for more than a week.

Ms Baxter took great pains to point out that the new confirmed case "had absolutely no contact between the case of the ISS contractor who was diagnosed earlier this week, and this employee".

"Our employee followed the correct procedure of staying home when unwell, seeking a COVID-19 test and promptly advising Metro of the positive test result," she said.

It is not known how the employee came to contract coronavirus.

The fresh positive comes as Victoria had 41 new COVID-19 infections on Saturday, the highest number of daily cases since early April, with Victoria’s Deputy Chief Health Officer admitting she was "very concerned" about the surge.