Police said the deceased included four women and the bus driver. All the deceased have been identified.
The condition of six of those injured is stated to be critical. All the injured have been admitted to different hospitals in the district.
Malappuram District Collector K Biju told PTI that 13 persons were killed and 29 injured in the accident.
The mishap occurred when the driver lost control of the mini bus while trying to overtake another vehicle after which it hit a tree, overturned and fell 25 feet down on another road.
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Preliminary reports indicated overspeeding as the cause of the accident.
A girl student, who escaped unhurt, said she heard loud sound of tyre burst before the bus rammed the tree and plunged. She also said bus was moving at a high speed when the mishap occurred.
An injured old man told reporters from his hospital bed that he too had heard a similar sound before the bus overturned.
Chief Minister Oommen Chandy, who termed the incident as the worst in Kerala, has rushed to the accident site.