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Train passengers fought back panic as carriages had to be evacuated when smoke was seen billowing from four carriages.
A fault with the shoe gears was blamed for the incident near Hither Green on the 7.17am service from Gravesend to Charing Cross.
Passengers on board the train pulled the emergency alarm and the train came to a stop.
They then evacuated onto the switched-off track or the platform, depending on which carriage they were in.
Buses replaced services between Dartford and London Bridge via Sidcup, and services were diverted via Bexleyheath.
The lines were re-opened at 10am with some knock-on delays. Services were back to normal by 11:45am.
Mark Joyce, of Wellington Street, Gravesend, was on his way to work in Croydon.
He said: “People in the carriage in front of ours started to get up and tried to make their way into our carriage.
“I don’t think the driver was aware that the carriage was on fire. He could only tell when the fire was blowing down the train" - passenger Mark Joyce
“For a split second there was a bit of panic and people started trying to run down the train. It was quite busy because it was rush hour.
"Then some of the passengers started telling everyone to calm down and we opened the emergency exits.
“I’m not sure that the driver knew what was going on because he said we’d be leaving shortly.
“People were helping each other down from the carriage, one of two people took control of the situation and we walked to Hither Green station. It took less than a couple of minutes.
“I don’t think the driver was aware that the carriage was on fire. He could only tell when the fire was blowing down the train.
“Once I was outside I was fine. A few people weren’t very comfortable but others were fine.
“No one came and spoke to us from Southeastern; it was more just passengers helping themselves.
“Once on the platform, people just crossed the bridge to another platform and tried to get another train into London.”
A spokesman for Southeastern said: “This was an understandably distressing event for the passengers onboard the train this morning.
"Thankfully we’ve had no reports of any passengers injured.
Video: Passengers evacuated after smoke comes from under carriages. Video: BublzMedia
"We’re fully investigating the cause of the problem to make sure this doesn’t happen again– but we understand the shoe gear overheated, causing a lot of smoke to billow out from under the train.
"Station staff rushed to assist the passengers onboard and staff from Network Rail’s nearby depot assisted passengers on the ground to evacuate through the depot.”