Police and firefighters wearing protective equipment carried out two complete sweeps of the building but failed to find anything.
However, a statement from the Met Police said: "A subsequent search of the airport led to the discovery of what is believed to be a CS gas spray,” Sky News said.
"Whilst the cause of the incident has not yet been confirmed, officers are investigating whether it was the result of an accidental discharge of the spray.
"Enquiries continue. This is not being treated as a terrorist-related incident. At this early stage officers believe that the spray may have been discarded by a passenger prior to check-in."
London City Airport evacuation linked to CS gas spray
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