Bruce Adamson, who took up the six-year post in May, said more teachers would be needed for schools to become more supportive.
He told the Times Educational Supplement Scotland: “To have proper pupil participation in learning delivers great outcomes but it requires additional teachers and support and investment - but it’s a good investment and it saves money because you have less pupil disruption, and a happier workforce and better outcomes - not just education outcomes.
“The teachers know the children better so they can pick up on issues and intervene early so you are going to save money in the health system - particularly around mental health - and the criminal justice system.”
Labour said his comments back their call for the Scottish Government to increase investment in education.
The party’s education spokesman Iain Gray said: “This is an important intervention from the commissioner, particularly about the impact increased teacher numbers can have around child health and the criminal justice system.
“Labour has said for years that the most important economic investment a government can make is education. Yet since the SNP came to power there are 4,000 fewer teachers in our schools.”
He said the Scottish Government’s claim that its top priority is education is “simply not a credible claim”, and the “real reform our schools need is more funding”.
Scottish Green education spokesman Ross Greer said: “These comments from the Children’s Commissioner are in line with what teachers, parents and the Greens have been telling the Scottish Government for some time.
“A decade of cut budgets has resulted in 4,000 fewer teachers and hundreds of lost specialist and support staff.
“The SNP needs to ditch its plans for a governance overhaul that no-one asked for, listen to Bruce Adamson and give councils the money they need to get teachers back into classrooms.”
The Scottish Government is implementing various education reforms designed to address the attainment gap and lift standards, which include targeted funding for deprived areas, direct cash for headteachers, and new educational regions to share best practice among schools.
A Scottish Government spokesman said: “We agree that teacher numbers and good pupil-teacher relationships are essential to a successful education system. That is why we have invested £88 million this year alone so every school has access to the right number of teachers.
“This investment has enabled local authorities to maintain the pupil teacher ratio and halted a period of steady decline in teacher recruitment by councils, resulting in 253 more teachers last year - the first substantial increase since 2007.”
He said more than £3 million is being made available to train an extra 371 teachers in 2017-18 alongside £1 million for universities to help develop new routes into teaching, and last year’s recruitment campaign helped drive a 19% increase in PGDE student intakes to Scottish universities compared to 2015.