In a speech to the think-tank Demos, she said schools and teachers had failed pupils in the "middle years" of compulsory schooling. Research shows that thousands of pupils are performing less well at the end of their first secondary year than they were at the beginning, and many more fail to progress.
Prime Minister Tony Blair is expected to underline the importance of the message today when he echoes the promise to focus relentlessly on the middle years during a visit to a northern secondary.
Ministers believe livelier teaching at key stage 3 will help to cut truancy, improve behaviour and prevent young teenagers drifting into a life of crime. Ms Morris blamed lack of pace and focus in teaching for a dip in achievement and a rise in disaffection and disengagement.
She laid out how KS3 would be overhauled under the new mantra of "standards, behaviour, choice".
Ms Morris's tenure is likely to be judged on the programme, which includes the pound;470 million ks3 reforms, a push to improve parental responsibility, and more "sin bins", specialist schools and city academies. The reforms are a response to pressure on the Government to curb spiralling street crime which sparked a Downing Street inquiry on Wednesday.
Home Secretary David Blunkett made it clear that schools must welcome police on site to identify problems and take early action and support police truancy sweeps.
Ms Morris said: "Some of the biggest increases in crime statistics, particularly street robbery, relate to 11 to 14-year-olds, with the threat that poses both to their own future life chances and the sense of cohesion and security in their own communities. The social cost is clear."
Last year The TES revealed a clear connection between absence from school, particularly where parents turn a blind eye, and crime rates. Nearly half of all permanent exclusions are in the first three years of secondary school.
KS3 standards have caused concern since national tests at 14 began a decade ago. About 200,000 pupils fail to make the grade at 14.
Since September, English and maths departments have been following government-designed KS3 lesson plans, but their ability to improve performance and increase motivation is unproven, particularly among children who failed to make the grade in primary school.
However, Ms Morris said test scores at 14 would be boosted: "This autumn we will see the first evidence of real gains in improved national curriculum test results."
The predicted rise would coincide with the publication of the first KS3 league tables in England.
A Department for Education and Skills spokesman said teachers were not expected to bear the burden alone. He said parents also had to face up to their responsibilities. Other departments, including health and transport, are expected to produce anti-crime policies.
Ms Morris said: "Turning around learning and motivation in the middle years is probably the toughest challenge, but this is what it is going to take to reform secondary education."