Police are currently negotiating with the nine activists, who have locked themselves together after apparently swimming across the Thames to gain access to the Royal Docks site.
Flights in and out of the airport were seriously affected.
A Scotland Yard spokesman said: “We were called at around 5.40am to reports of a number of protesters who made their way air-side.
“There are currently nine protesters on the runway at the airport. They have erected a tripod and have locked themselves together.
“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.
“No arrests have been made at this stage.”
It is the latest demonstration involving the anti-racism activists, who brought traffic to a standstill outside Heathrow Airport - and carried out similar protests in cities around the country - in a co-ordinated day of action last month.
The campaigners, whose international movement was set up following the killing of black teenager Trayvon Martin in Florida four years ago, said Tuesday’s action was taken “in order to highlight the UK’s environmental impact on the lives of black people locally and globally”.
In a statement, the protest group’s UK division cited expansion plans at the airport as the cause of their action.
They said: “Recently London City Airport was given approval to expand its capacity, a move that consigns the local community in Newham to further deterioration of their environment. The average salary of a London City Airport user is 136,000 euros (£114,000) and 63% of them work in business, finance or other business services.
“It is an airport designed for the wealthy. At the same time 40% of Newham’s population struggle to survive on £20,000 or less. When black people in Britain are 28% more likely to be exposed to air pollution than their white counterparts, we know that environmental inequality is a racist crisis.”
An airport spokesman said: “We’re currently experiencing disruption to all flights due to protesters at the airport. Police are currently on the scene.”