It followed an outbreak of the virus which forced the closure of Rail Gourmet’s Edinburgh premises and 12 of its 60 staff testing positive for coronavirus.
The Scotsman understands that only close contacts of those who contracted Covid would have been offered tests as a matter of course.
The Rail, Maritime and Transport union (RMT) accused the firm of “silencing and disciplining hardworking staff who dare to raise genuine safety concerns”.
It has threatened to ballot staff for industrial action unless the charges are dropped.
However, Rail Gourmet said it was investigating claims that staff had “knowingly come to work with Covid-19”.
The Scotsman revealed last Saturday that a manager had emailed staff: “When you book a test, please put down that you have at lest one symptom so you actually get a test done”.
An insider said the email was "telling us to make up we had symptoms to get a test”.
Rail Gourmet admitted the instruction should not have been issued.
It said: “We fully recognise that on this occasion, the wrong advice was given to our team.
"We will be reinforcing the correct protocols to our colleagues.”
The RMT said the two staff, who had contracted Covid-19, were facing disciplinary hearings “for raising related health and safety concerns while they are in isolation and suffering significantly from the effects of the illness”.
The Scotsman has learned they are being investigated for “breach of trust” and “breach of health and safety concerning Covid 19”.
One of the workers is an RMT industrial representative.
The union said it was already preparing a strike ballot among Rail Gourmet staff at Paddington in London after a worker was suspended for raising similar Covid-19 concerns.
General secretary Mick Cash said: “A dozen catering workers at Rail Gourmet in Edinburgh have tested positive for Covid-19 but the company are only interested in their loss of revenue and silencing and disciplining hardworking staff who dare to raise genuine safety concerns.
“Following hot on the heels of a similar episode at the Paddington depot where we are already balloting for local strike action, it is clear this has now become the company’s policy.
“Rail Gourmet would be better off spending their energy resolving the genuine Covid-19 health and safety concerns of staff rather than hounding RMT members for raising them.
“I am writing to Rail Gourmet to inform them that unless the charges are dropped we will declare a company-wide dispute and ballot our members for industrial action across the entire operation.”
A spokesperson for Rail Gourmet said: “The health and safety of our colleagues and customers is paramount to us, and we have strict Covid-19 related protocols in place to protect them.
“Following allegations that team members in our Edinburgh service centre had knowingly come to work with Covid-19, we launched an internal investigation into the validity of these claims.
"The investigation remains ongoing and as soon as we reach our conclusions, we will be confirming our findings directly to the colleagues in question.”