The new rules have been so fiercely enforced that a female train driver recently locked herself in a toilet cubicle to phone for help after she was allegedly approached by two Metro officers while at her personal doctor's clinic in Frankston.

Melbourne's rail operator introduced its new policy in March for drivers who sustain physical injuries on the job and shock or trauma from near-miss collisions, according to a memo from Metro management obtained by The Age.

But the directive has raised concerns over allegations of intimidation and employment policies that infringe on workers' private lives and personal choices.

It is understood that Metro held a meeting with the Rail, Tram and Bus Union on Wednesday morning to discuss possible changes to its rules, but the union said its concerns had not been addressed.

Metro spokeswoman Larisa Tait said rules requiring a company-chosen doctor for workplace injuries were based on its duty of care. "These practitioners are familiar with the role and health requirements of a driver, as well as common injuries sustained on the job," she said. Metro was "constantly reviewing" its policies to determine where improvements could be made.

The union said it had received troubling reports of employer heavy-handedness, including the July incident when two Metro managers allegedly attended the private medical clinic in Frankston. The female driver, injured after falling between a carriage and platform that day, was being treated there for leg wounds.

The woman's union representatives said she felt so threatened by the managers, who were trying to make her to go to a company doctor, that she raced to the women's toilets and called union officials. The managers are also accused of cancelling a taxi the woman had booked to go home.

"In the end, we asked for the phone to be given to the managers and we said if you don't desist we will call the police," RTBU locomotive division secretary Marc Marotta said.

The driver, aged in her 30s, has returned to work but is now believed to be facing disciplinary action over her refusal.

In a separate allegation, Mr Marotta said another female driver was stood down without pay in late August for refusing an appointment with a therapist selected by Metro after a close call with a pedestrian on the tracks.

The union has held two meetings with its Metro employee members in recent weeks and says it has considered taking legal and industrial action.

"We have written to the company saying there are certain occasions when management should assist employees in attending health practitioners but it must be on a case-by-case basis," Mr Marotta said.

Enrico Burgio, an associate with Maurice Blackburn, said there was a "growing trend" of incursion into employees' private lives, and "one-size-fits-all" policies such as Metro's raised legal questions.

"We say a blanket policy for all injured employees to consult company doctors is unlikely to be lawful," Mr Burgio said. "It intrudes into people's personal medical choices. It is an expected right that they should be able to choose."

But Trish Low, of law firm Herbert Smith Freehills, said businesses were within their rights to nominate health practitioners in the event of workplace injuries, and it was not uncommon to do so.

"In the vast majority of cases, the process is entirely uncontentious," she said. "In my experience, if there is a legitimate reason for their objection, employers will consider alternative practitioners."

Ms Low said employers often had a number of practitioners who had previously conducted workplace inspections and were familiar with specific workers' duties.

"This additional knowledge and experience puts such practitioners in a better position to properly assess an employee's fitness for work than a practitioner who has no understanding or experience of the job or workplace," she said.