The Metropolitan Police said the operation in east London was "intelligence-led" and resulted in the arrest of four people.
Two of the arrests were on suspicion of "conspiracy to facilitate the escape of an individual from custody".
Scotland Yard said in a statement: "Officers from the Met Police Organised Crime Command and Specialist Firearms Operational Command Unit have this morning arrested four men as a result of a pre-planned intelligence led operation.
Witnesses described the man who was shot as sitting alone in a black Audi when he was surrounded by armed officers.
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There were no reports of any other injuries.
The UK's Independent Police Complaints Commission said investigators were at the scene overseeing initial accounts given by the officers involved.
The Met added the Directorate of Professional Standards, its internal investigator, had also been informed and confirmed the incident was not related to terrorism.