Extra security staff are at stations on Govia Thameslink Railway (GTR) routes to protect staff from "unhappy customers".
GTR passengers have faced train delays and cancellations since new timetables were introduced in May.
The firm issued a security brief to staff, leaked by the RMT union, on customers who "vent their frustration".
It advises staff to "remain calm and de-escalate the situation by being apologetic and showing empathy".
Rail enforcement staff are being deployed to help station staff and to act as a deterrent, and more security staff are being employed to support staff, GTR said in the letter.
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'In daily danger'
RMT general secretary Mick Cash said: "This notice issued to GTR to staff shows the reality of [transport secretary Chris] Grayling's railway.
"That such a notice has had to be issued at all demonstrates the daily danger that staff are being put in as a result of Grayling's incompetence.
"If putting railway staff at risk in this way is not a reason to resign then what is?"
GTR, which runs Great Northern, Thameslink and Southern said it would not be commenting on the leaked document.
A spokesman for the Department for Transport said: "This has been a very difficult time for rail users, but we urge them to remain patient and avoid taking out their frustrations on staff who are working hard to put things right as quickly as possible.
"There will now be an independent inquiry to determine how this went so badly wrong and to make sure this does not happen again.
"The Transport Secretary will also investigate whether GTR has breached its contract and won't hesitate to take tough action if it has been negligent."