Data obtained under the Freedom of Information Act by the mental health charity MIND showed 39,883 recorded incidents of all kinds of physical restraint in mental health trusts during 2011/12, resulting in at least 949 injuries to people with mental health problems.
The charity said there was "huge variation" between trusts in the use of all types of physical restraint.
Surrey and Borders NHS Foundation Trust reported just 38 incidents over the year while Tees, Esk and Wear Valleys NHS Foundation Trust reported 3,346.
The charity said the figures for overall physical restraint incidents, including face-down incidents, were compiled from answers provided by 51 mental trusts.
More than half of the responding trusts, or 27, said 3,439 of the incidents were of face-down restraint, a potentially life-threatening form of restraint, according to Mind.
Northumberland, Tyne and Wear NHS Foundation Trust recorded 923 incidents of face-down restraint and Southern Health NHS Foundation Trust 810, according to the charity's figures.
A separate survey by Mind of 375 frontline healthcare staff involved in physically restraining people with mental health problems, showed almost a quarter, 22%, had not had face-to-face training on physical restraint techniques in the last 12 months. More than four in ten, or 42%, according to the charity, said that with hindsight, they felt that restraint had sometimes been used "inappropriately".
Paul Farmer, Mind chief executive, said: "Physical restraint can be humiliating, dangerous and even life-threatening and the huge variation in its use indicates that some trusts are using it too quickly. Face-down restraint, when a person is pinned face-down on the floor, is particularly dangerous, as well as extremely frightening to the person being restrained. It has no place in modern healthcare and its use must be ended."
A spokeswoman for Tees, Esk and Wear Valleys NHS Foundation Trust said: "The number of incidents may seem high. However, we are one of the largest mental health and learning disability trusts in the country... Our staff are fully trained in using a range of techniques to manage people with challenging behaviour and they adopt an individualised approach for each patient. Physical restraint, using nationally accredited techniques, is only used as a last resort."