Activists from the international group "Black Lives Matter UK" claimed responsibility for the disruption at the airport, Efe news reported.
The activists tweeted, "At London City Airport a small elite is able to fly, in 2016 alone 3,176 migrants have died or gone missing in the Mediterranean #Shutdown."
According to the police, nine protesters managed to make their way onto the tarmac after sailing across the Royal Docks in a boat and locked themselves together on the runway, the daily Mirror reported.
The group formed about four years ago after the fatal shooting of African-American teenaged Trayvon Martin in the US has been staging anti-racism protests.
The airport apologised to passengers for the disruption and said that flights due to land have been diverted and services would resume as soon as possible.
London City Airport is popular with bankers and business people due to its close proximity to the capital's financial district.
An estimated 4.3 million passengers used the airport last year.
