A casualty on the tracks was reported at the station in Deal Porters Way just after 10am today (March 10).
Officers and London Ambulance Service crews attended and a man was taken to hospital for treatment.
His injuries were assessed as non-life threatening.
The incident is not thought to be suspicious.
All lines between Dalston Junction and Surrey Quays have closed as the incident is being dealt with.
Major disruption is expected until 1pm.
If you need to talk to someone, you can contact the Samaritans at any time for free on 116 123.
A spokesperson for British Transport Police said: “Officers were called to a report of a casualty on the tracks just after 10am today (10 March) at Canada Water Underground Station.
“Officers and paramedics attended and a person has been taken to hospital with injuries not thought to be life changing or threatening.
“The incident is not thought to be suspicious.
A London Ambulance Service spokesperson said: “We were called at 10.04am today (10 March) to reports of a person hit by a train at Canada Water Station, SE16.
“We sent resources to the scene, including an ambulance crew, a paramedic in a fast response car, an incident response officer and paramedics from our hazardous area response team (HART).
“We also dispatched London’s Air Ambulance.
“Our first paramedics arrived in five minutes.
“We treated a man at the scene and took him to a major trauma centre by road.”
