Image copyright @ukblm
Image caption Black Lives Matter UK initially claimed the protest through a series of tweets
Black Lives Matter UK said the action was taken in order to "highlight the UK's environmental impact on the lives of black people locally and globally".
A statement said: "Whilst at London City Airport a small elite is able to fly, in 2016 alone 3,176 migrants are known to have died or gone missing in the Mediterranean.
"Black people are the first to die, not the first to fly, in this racist climate crisis.
"We note, however, that the UK is willing to charter special flights to remove black people from the country based on their immigration status."
Media captionWhy Black Lives Matter closed City runway
Speaking to BBC London, group member Joshua Virasami added: "The community where this airport is is a predominantly black community.
"In Britain, 28% of black people are more likely to be exposed to air pollution... being in closest proximity to the industries causing climate change."
He added the disruption to flights was "a very small inconvenience when you think about the consequences for black communities daily" and the protesters would remain on site "as long as feasibly possible".
Scotland Yard said it was investigating how the protesters got on the runway - including the suggestion that they swam across the River Thames or used a boat.
When asked how the protesters gained access, Mr Virasami said "I'm not in a situation to say... but one can use their imagination".
Image copyright @UKBLM
London City Airport passenger Hannah Moore, from Wandsworth, south-west London, was due to fly to Amsterdam.
She said: "It's chaos. There's a huge queue outside the airport. I managed to get in. We've been told to watch the boards.
"I have an important business meeting to attend in Amsterdam. I've told them I might not make it."
Media captionHas Black Lives Matter been hijacked?
Casey Collins, who was due to fly to Luxembourg, said customers had initially assumed the delays were related to IT glitches at Heathrow and Gatwick.
He said: "The problem was that there were only two or three staff there. People were behaving themselves, they know it was not the airport's fault, but for a time it was a bit chaotic."
He said passengers were offered refunds for cancelled flights, while delayed passengers were given refreshment vouchers.
Image copyright Aimee Roweth
The Met said all nine arrests were on suspicion of aggravated trespass, being unlawfully airside and breaching London City Airport bylaws.
A London City Airport spokesperson added: "We apologise to passengers for any inconvenience to their journey."
The airport is popular with bankers and business professionals due to its proximity to Canary Wharf in London Docklands.
Last year, a record 4.3 million passengers used the airport.