A matatu belonging to Ummoinner Sacco was on Wednesday night burnt after it hit and killed a boda boda operator along Jogoo Road.
The driver escaped the scene after the incident when he noticed the crowd was turning violent, and is being sought.
Police said the driver, identified as Elijah Mwangi, was overlapping to beat traffic jam that was building up when he ran over the rider at the Doonholm roundabout.
A mob gathered and burnt down the matatu after the passengers had disembarked, Nairobi police boss Japheth Koome said. Koome warned against the trend saying investigations into the incident had been launched.
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"We understand there was a fatal accident that escalated to arson. We don't encourage such behaviour and culprits will no be spared," he said.