The nose wheel of the British Airways jet broke on landing after travelling from Amsterdam as the undercarriage failed.
The 67 passengers and five crew on board the flight were evacuated safely but two people have been taken to hospital.
Six ambulances were sent as a precaution as well as a number of fire engines and police cars.
Eye witness Alistair Grant told Sky News: "I'm just opposite City Airport and there are about 20 fire engines and ambulances on the runway. Police have blocked everything and are diverting traffic.
"The whole of the front undercarriage has failed but apart from that it's not in bad shape.
"It's a very chilly night out here so luckily the plane didn't skid into the dock which is very close. There's people all around the area blocking off traffic."
He added: "To me it looks like police and fire crew have worked very diligently. As for the shock and trauma of passengers I can't say."
One passenger who was stuck in the departure lounge waiting to catch a flight to Switzerland said security had moved everybody away from the windows and set up a barricade so nobody could see what was happening on the runway below.
A number of arriving flights have been diverted while the remaining flights of the night have been cancelled.
The website for London City Airport said: "Due to incident, London City Airport's runway is now closed. Please contact your airline for airline for the latest information.
"London City Airport apologise for any inconvenience caused."