Speaking at the Holyrood Seminar, organised by the Scottish Parliament's education committee, Ms Marshall said: "They are human beings with human rights; they are here, and they need and are entitled to our care and protection."
She added: "The attempt to define some asylum-seeking children, particularly those detained in the Dungavel immigration removal centre, as wholly the responsibility of the Home Office, risks defining children out of their childhood," Ms Marshall said.
She had become increasingly concerned about the way families were being removed from their homes in "dawn raids". "I was very pleased that the Scottish Executive and the Parliament decided to 'own' these children," the commissioner said.
Ms Marshall warned of the dangers in allowing children to be "divided up, shared out and defined out of their childhood" in the contexts of family law reform, child protection and the treatment of 16-18s, particularly those in the care system.