It is scheduled to take command of trains on some of the UK's busy intercity routes by the 2020s.
The system is already used in other parts of the world and there are no reported cases of it being affected by cyber-attacks.
In fact, it is designed to make networks safer by reducing the risk of driver mistakes.
But Prof Stupples - an expert in networked electronic and radio systems at City University in London - said if someone hacked into the system they could cause a "nasty accident" or "major disruption".
"It's the clever malware [malicious software] that actually alters the way the train will respond," he explained.
"So, it will perhaps tell the system the train is slowing down, when it's speeding up."
"Governments aren't complacent", the professor added.
"Certain ministers know this is absolutely possible and they are worried about it. Safeguards are going in, in secret, but it's always possible to get around them."
He added that he had spoken up to raise awareness of the threat.
"We keep security arrangements under constant review to take account of the threat and any new challenges we face," responded a spokeswoman for the Department of Transport.