The incident occurred around 4.15 AM while backing the rakes from the yard to platform during shunting works, PRO, Southern Railway, R Gopinath said.
The derailment led to a delay of nearly one-and-a-half hour in train's departure.
The train which was scheduled to leave at 5 AM, left Kannur at 6.35 AM with a spare engine.
However, traffic in the route was not affected due to the derailment, he added.
A break down van with crane has been pressed into service to set the engine right, the official said, adding that none were injured in the incident.
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