The strategy will be headed by a national behaviour director, who will be supported by a network of regional directors.
From September, all schools will have to draw up intervention programmes to engage 12 and 13-year-olds who are falling behind or losing interest.
Local authorities will appoint behaviour experts to train teachers and go into schools to offer advice on how best to deal with problem pupils.
Last month, Education Secretary Charles Clarke announced the Government's strategy on behaviour and attendance in schools. A total of pound;470 million will be spent over three years to halt the daily disruption of classes in some schools.
Des Dunne, director of the KS3 science strategy, said: "The behaviour strand will be about engaging and motivating and providing guidance to schools to deal with the children who are falling by the wayside."
An "assessment for learning" strand of the KS3 strategy will also be developed. The technique adopted at King's College, London University, involves less testing and marks out of 10 and more instant feedback from teachers. Pupils are encouraged to judge their own work as well as that of their classmates. Teachers will receive training in March 2004.