The Severn Tunnel was temporarily closed on Wednesday evening following an incident in which passengers reported seeing "flames" from the windows.
ITV Wales reporter Mike Griffiths, who was travelling on the train at the time of the incident, said there was a loud noise followed by passenger reports of "flames" outside, a burning smell and a shattered window.
The train stopped and the Severn Tunnel, which links South Gloucestershire to Monmouthshire, was closed to allow investigations to take place.
A Great Western Railway said the train came to a halt due to an "engine fault".
A spokesperson said an investigation into what happened was currently ongoing, but there was no present evidence of a fire.
Neil Mukerji, a student from Cardiff, was travelling from Bristol and was in the train's second carriage.
He reported seeing flames and said he could even feel the heat coming from them.
He said: "We were just going through the Severn Tunnel and we just saw fire coming up for around five or ten seconds and then I felt a burst of heat on the left side of my face and then we started smelling smoke.
"The train started slowing down and we exited the tunnel, we saw the woman next to us and her window had actually smashed."
A National Rail alert published on Wednesday evening confirmed there was disruption to the line, and said a "safety inspection" was taking place along the track between Patchway and Severn Tunnel.
National Rail said the line was clear again by 01:00 on Thursday morning.
'An engine fault'
A spokesperson for Great Western Railway said: "The 1723 Portsmouth Harbour to Cardiff service came to a stand at Severn Tunnel with an engine fault. The cause of the fault is currently being investigated.
"Unfortunately, this closed the line into/out of south Wales while a track inspection was carried out, significantly delaying services through the area. Customers were either taken forward using a diversionary route, or by replacement bus service.
"We are really sorry to those caught up in the disruption. Those affected may be entitled to compensation and we would urge them to get in touch at https://www.gwr.com/help-and-support/refunds-and-compensation/delay-repay".
Want a quick and expert briefing on the biggest news stories? Listen to our latest podcasts to find out What You Need To Know...