Up to 16,000 passengers are expected to be affected by the airport's closure, a spokesperson told the BBC.
Police were called to the scene at the George V Dock, North Woolwich, just after 5am on Sunday.
London City Airport has been shut after Second World War ordnance was discovered in the River Thames.
"Overnight, officers have been helping to evacuate properties within the exclusion zone and police are working with the local authority to provide residents with temporary emergency accommodation and the appropriate support".
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Passengers have been advised not to travel to the airport until further notice, according to a statement on the London City Airport's website.
The police said that the decision to close the airport had been taken "to ensure that the ordinance can be safely dealt with whilst limiting any risk to the public".
Road cordons have also been put in place with drivers warned about disruption to their journeys if travelling through Newham.
"The operation to remove the ordnance is ongoing in partnership with our colleagues in the Royal Navy".