Armed officers were in Bracknell Close, Wood Green, at about 09:00 GMT when a man received gunshot wounds, police said.
The Met said the operation was "intelligence-led" but not related to terrorism.
It added the Directorate of Professional Standards - its internal investigator - had been informed.
An air ambulance was called to the scene but the man was confirmed dead shortly before 10:30 GMT.
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There were no reports of any other injuries.
One Twitter user reported seeing "police everywhere" and a "medical helicopter".
A man shot during a police operation in north London has died, Scotland Yard has said.