The bill, which is currently going through parliament, outlines plans to replace SEN statements with single education, health and care plans.
These plans would require all local services to co-operate on SEN provision, but the current wording of the bill states that the plans will be suspended if a young person enters custody.
Speaking in parliament, youth justice minister Jeremy Wright said that there are elements of SEN support that “cannot be taken with the young person into a custodial setting”.
He said the focus is instead being placed on ensuring that “the transition into, and out of, a custodial setting is managed appropriately for young people”.
The Special Educational Consortium and the Standing Committee for Youth Justice have previously called for young people in custody to be included in the reforms.
Wright said that the government is seeking to improve its work with young people with SEN in custody through its consultation on transforming the youth custody system.