Armed officers and explosives teams with sniffer dogs were seen patrolling in the Liverpool Street and Moorgate areas.
Witnesses said trains were running as normal but roads near the stations were closed, Independent reported.
Alex Holmes, founder of the Anti-Bullying Ambassadors group, filmed officers patrolling with guns, mounted police and sniffer dogs in the road outside his offices.
"We are being asked not to leave the building," he wrote on Twitter. "The road in front of us is closed leaving to Liverpool Street."
City of London Police said officers had been deployed to Wilson Street "following a report of a suspicious package in the area".
A spokesperson urged members of the public to avoid the area around Moorgate, South Place, Eldon Street, Blomfield Street and South Street as checks continued.
Police said the item was later found to be non-suspicious and the cordons were lifted.
The operation came as British security services remain on high alert following an attempted bombing on a London Tube train last week.
The national terror threat level was raised to "critical" after the blast, which injured 30 people, but has since returned to "severe", meaning further attacks are considered highly likely.
