Following the discovery of a World War Two ordnance in King George V Dock as part of planned development works, a 214m exclusion zone has been implemented as a precaution by the Met Police.
There will be disruption to inbound and outgoing flights, the police spokesman said.
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There is also no service on the DLR between Pontoon Dock and Woolwich Arsenal due to the discovery.
London City Airport said all flights in and out would be cancelled, and urged passengers not to travel to the airport and their airlines for further information. "Passengers are advised not to travel to the airport until further notice".
"I recognise this is causing inconvenience for our passengers, and in particular some of our local residents".
Metropolitan Police and the Royal Navy are working together to remove the bomb from its location.
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It has been reported that the airport closure triggered cancellation of all flights affecting up to approximately 16,000 passengers.
Operations to remove the bomb are ongoing.
Police set up a 214-metre (700ft) exclusion zone at 10pm on Sunday to decrease risks to the public after its origin was confirmed by specialist officers and the Royal Navy.
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