Gove, who left government in July following his failed bid to win the Conservative leadership contest, will chair an advisory board supporting a major two-year drive by the Howard League for Penal Reform.
The charity said the programme will explore best practice within the police service and the residential care sector, in relation to keeping as many boys and girls as possible out of the criminal justice system.
The launch of the programme comes five months after the charity said that research it conducted suggested there is a systemic problem across England and Wales that leads children's home staff to resort to the police, often over minor incidents.
It said that among 13- to 15-year-olds, children living in children's homes are almost six times as likely to be criminalised as looked-after children in other placements - and almost 20 times more likely to be criminalised than a child not in care.
Frances Crook, chief executive of the Howard League for Penal Reform, said: "We are delighted to announce this important programme of work, which will build on our existing expertise on the policing of children and respond to concerns that police forces themselves have highlighted to us on the criminalisation of children in residential care.
"There are two major questions we shall seek to answer. Firstly, how can children's homes be encouraged to manage children's behaviour without recourse to the police?
"And secondly, in those cases when the police are called out to homes, what can be done to avoid a child being unnecessarily criminalised?
"I am particularly pleased to welcome the involvement of Michael Gove, who has spoken so eloquently in the past about doing the best for troubled children in our society."
