Protesters swam across a dock and "occupied" the runway at London City Airport, Sky News reported.
The activists were from the Plane Stupid movement, campaigning against expansion in the aviation industry, according to media reports.
The airport said on Twitter all flights were facing disruption.
"Police are currently on the scene," it added.
British Airways said it was checking in customers as normal at Heathrow and Gatwick, London´s two biggest airports, but it was taking longer than normal and encouraged people to check-in online before they reached the airport.