Flights from the airport, which lies a few miles east of the Canary Wharf financial district that mostly handles short-haul flights to business destinations in Europe, were disrupted and some arrivals were diverted according to the airport's website.
"Officers are currently on scene and are negotiating with them. We are awaiting the arrival of specialist resources that are able to 'unlock' the protesters," said police.
The campaign group Black Lives Matter said its activists were behind the protest.
"London City Airport was shutdown," it said in a statement.
The British arm of "Black Lives Matter", which started in the United States as a reaction to fatal shootings of black people by white US police officers, said it wanted to highlight Britain's environmental impact on the lives of black people locally and globally.
Ten people from Black Lives Matter were arrested in August after they blocked the main road to London's Heathrow Airport.
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