The train is blocking the line between Castle Cary, Somerset, and Westbury, Wiltshire. Network Rail said services will be affected for at least 48 hours.
It was pulling 38 wagons filled with stone and ballast, seven of which derailed on Monday.
The accident has caused significant damage to track and equipment.
Services from Taunton to Westbury and between Weymouth and Westbury are severely disrupted.
One commuter told the BBC: "I'm travelling up to London for a series of meetings.
"I will just have to wait and see how long it takes as a result of the disruption."
Latest on this story and other news from Wiltshire and Somerset.
Operator GWR said trains will be amended or cancelled, with replacement road transport provided where required.
A Network Rail spokesman said: "We are working closely with GWR and South West Trains to put in place contingency plans... including diverting London-West of England services via Bristol.
"The derailment is significant with the line currently blocked and likely to remain out of use for at least the next 48 hours."
The derailment of a freight train is continuing to cause "severe disruption" to rail services in the west of England.