The Neglected Children's Department was a part of the Chief Secretary's Department but with its own Secretary. The offices were in the New Town Charitable Institution, an invalid depot a few miles from the centre of Hobart, in the same building as the Boys' Training School. Between 1896 and 1912, the Secretary of the Department was also the Administrator of Charitable Grants as well as the Manager of the Boys' Training School, the Invalid Depot in Launceston, and the New Town Charitable Institution. The close relationship between the Charitable Grants and Neglected Children's Departments may explain why, in 1907, when the Public Service Act proclaimed the first list of departments, Charitable Grants appeared but Neglected Children did not. Technically, this meant that it was not really a department. Even so, the government treated it as one.

George Richardson was the first Secretary, appointed in 1896. When he became Commissioner of the newly created Police Department in 1898, Frederick Seager replaced him. In 1911, the charitable departments were brought under the direct jurisdiction of the Under-Secretary, HE Packer and the offices moved into Hobart. Packer died in 1914 and D'Arcy Addison replaced him.

The Secretary of the Department was the guardian of all wards of state. He decided whether to place them in a receiving home, the boarding out system, in a training school, such as the Boys' Training School, a voluntarily run children's home, or in an apprenticeship in which boys usually learned farm labouring and girls domestic service.The work of the Department included correspondence with children, especially older ones, their parents, foster parents, and employers.The Department also carried out inspections of the homes where wards of state lived. The officials maintained a separate file for each child that contained correspondence, inspectors' reports, and other information about his or her life. In 2013, these files are held by the Tasmanian Archive and Heritage Office.

One of Richardson's first acts was to abolish the Central Boarding Out Committee. In 1897, he took over some of their administrative responsibilities which led to a dispute. The Committee stopped holding monthly meetings until Richardson restored their powers. He did not and the Committee disappeared in 1898. After that, wards of state were managed by public servants. One advantage of this arrangement was that they knew the children personally.

Seager lived on the grounds of the New Town Charitable Institution where, according to Naomi Parry, the whole family helped destitute people who turned up at all hours of the day and night. This was important career preparation for the eldest son, Charles, who was appointed as a clerk in 1900. His father had pushed for the appointment, arguing that he was 'peculiarly adapted for the service required', and, since he lived on the premises would help with work after hours. Charles Seager went on to become the Chief Clerk and in 1923 the Administrator of Charitable Grants. In 1934, he became the Director of Social Services, retiring in 1941.

The Neglected Children's Department struggled for funds during Frederick Seager's administration. One difficulty was that many more children were committed than had been expected. In 1898, the Premier, Edward Braddon, said that, to save money, the Youthful Offenders, Destitute and Neglected Children's Act might have to be repealed. In 1902, a select committee was established to investigate the government's overall budget problems. One witness suggested that 'unprofitable' departments be abolished. He almost certainly meant the Neglected Children's Department, among others. After that, cost cutting led to a drop in the number of committals. This frustrated Seager who wanted to rescue more of the state's destitute children. He spent much of his time managing the tension between committing more children and saving money.

He was also frustrated by the terms of the Act which did not allow children to be committed solely on the grounds of destitution. Instead their parents had to be persuaded to surrender them as 'uncontrollable'.

In 1907, the South Australian child welfare activist, Catherine Spence, wrote that the number of children in the 'care' of the Tasmanian Neglected Children's Department was low compared to South Australia. She concluded that: 'Either the population is more virtuous or there are far less clear ideas as to what constitutes a neglected child'. Prompted by this criticism, Seager asked the government to commit more children. The Attorney-General, WB Propsting, responded in 1908 by setting up a committee to consider changes to the Act. Its members included Seager, a doctor, and representatives of the Children's Protection Society. They recommended widening the definition of a neglected child to one:

who is found begging, receiving alms, thieving in a public place, sleeping at night in the open air, wandering about at late hours, associating or dwelling with a thief, drunkard or vagrant, or a child, who by reason of neglect, drunkenness or other vice of its parents is growing up without salutary parental control and education, or in circumstances exposing such child to an idle and dissolute life or who is found in a house of ill fame or known to associate with or be in the company of a reputed prostitute, or who is an habitual prostitute, or an orphan and destitute, or deserted by its parents, or whose only parent is undergoing imprisonment for a crime, or who by reason of ill treatment, continual personal injury or grave misconduct or habitual intemperance of its parents, or either of them, is in peril of loss of life, health or morality, or in respect to whom its parents or only parent have been convicted of an offence against this act or under the criminal code, or whose home by reason of neglect, cruelty or depravity is an unfit place for such child.

This definition drew on Ontario's 1893 Children's Protection Act. It did not address Seager's concerns about children who were destitute. The definition was never used although the Children of the State Act 1918 included most of its ideas.

The Secretary of the Neglected Children's Department had the power to place children where he saw fit. Most were boarded out but some also went to the Boys' Training School, usually because they had committed an offence, and industrial schools. When they reached school leaving age, the Secretary apprenticed them, mainly as farm labourers if they were boys or domestic servants, if girls. This did not involve formal indentures and the Secretary remained the children's guardian.

Seager (and subsequent) Secretaries preferred the boarding out system to institutions. In 1909, Seager said that industrial schools 'fell far short of the requirements of motherhood' and that the 'motherly interest' that foster mothers took in the children made their training more effective. However, he could also be pragmatic. On one occasion, he placed neglected boys in the Boys' Training School to make up the numbers for farm work.

In 1911/12 the Departments for Neglected Children, and Charitable Grants were absorbed into the Chief Secretary's Department with the Under-Secretary assuming direct responsibility for the 'care' of the wards of state. The reasons for it are not clear but it is possible that the government no longer considered Seager competent. The Under-Secretary's administration appears to have created more confidence because the government increased funding to the Department and the number of committals rose.

In August 1912, Packer suggested that the Neglected Children's Department be moved to the Police Department which already administered the babies who came under the Infant Life Protection Act 1907. In 1916, there was a proposal to transfer the babies to the Neglected Children's Department. Neither took place. The children in the two Departments did not come together until the passage of the Children of the State Act in 1918.