Humberside Police confirmed the discovery at King George Dock in the city on Tuesday.
Paramedics said three people were taken to hospital and a further eight were checked over at the scene.
None of those found inside are thought to be in a life-threatening condition, a police spokeswoman said.
She said: "Officers are currently in attendance at King George Dock in Hull after a number of people have been found in a container at the dock.
"Some of those found are in need of medical treatment, although none of those are thought to be in a serious or life-threatening condition."
A spokeswoman for Yorkshire Ambulance Service said: "We were called to attend an incident at 11:33am on Tuesday March 3 at King George Dock in Hull.
"We sent two rapid response vehicles, three emergency ambulances, two doctors and our Hazardous Area Response Team to the scene.
"We transported three patients to Hull Royal Infirmary and eight patients were checked over on scene but didn't need conveying to hospital."