Controversial plans that would see children “warehoused” in a new generation of large-scale secure colleges for juvenile offenders will be confirmedon Monday .

Peers in the House of Lords had tabled amendments to the criminal justice and courts bill so that the colleges would exclude boys under the age of 15 and all girls. But the government will reject the amendments when the bill goes back before parliament.

The move will dismay prison reform groups, who are concerned by plans to create large units capable of holding up to 320 offenders, including girls and boys aged between 12 and 17.

The government believes the colleges will provide a more healthy environment for young offenders, one that is more like a school than a prison, and stresses that girls and younger boys will be protected because they will be held in separate, fenced-off blocks.

However, an alliance including the Howard League for Penal Reform and the Prison Reform Trust claims the colleges pose “serious and unprecedented safeguarding risks”.

Opponents point out that last year 95% of youngsters in custody were male and 96% were aged 15-17. In a secure college, this would see around 16 girls and 13 younger boys incarcerated with 291 older boys. “No child should be kept in a 320-bed warehouse, but particularly not the most vulnerable,” said Penelope Gibbs, who chairs the Standing Committee for Youth Justice.

“Girls and younger children need small, family-like secure homes where they know the staff and other children and feel safe. The numbers of children in custody have come down so significantly [that] the secure college is hardly viable. It looks as though they are only including girls and younger children in order for the sums to stack up.”

Justice minister Andrew Selous said the colleges would provide a pioneering approach to youth custody, with education at the centre. “By moving away from the traditional environment of bars on windows and giving these young people skills, qualifications and self-discipline we can help them turn their back on crime and become productive members of society,” he promised.

The Howard League questions how often girls and younger boys will be able to access the facilities on the main site if they are fenced off for their own protection. “I fear that in a decade the government will be left wondering why so much money was invested in such an ill-informed project,” said Enver Solomon, director of evidence and impact at the National Children’s Bureau.

There are suggestions that the Lib Dems are having doubts about the decision to include girls and younger boys in the colleges. A number of leading institutions, including the NSPCC and the Royal College of Psychiatrists, have opposed the plan, which is expected to cost £85m to roll out. It is anticipated that each place will cost under £100,000 a year to provide.