Around 500 children aged 10 and under were stopped and searched by the police in 2010, a recent Scottish Centre for Crime and Justice Research report found.
Use of stop and search has more than doubled in recent years with Scots estimated to be six times more likely to be stopped than people south of the border, but detection rates for offensive weapons are less than 2%, Edinburgh University research found last month.
Reports that the use of stop and search is "based on a desire to meet targets" have been described as "unacceptable" by the Together alliance for children's rights.
The alliance, which comprises Barnardo's, Children 1st, Children in Scotland, Circle Scotland, Includem and Mentor UK, have called for a review.
A Together statement said: "Recent reporting on the use of stop and search by police on children and young people has raised the worrying concern that its use is disproportionate and based on a desire to meet targets rather than an intelligence-based assessment of risk.
"This would be unacceptable and calls into question whether children and young people's rights, as enshrined in the United Nations Convention on the Rights of the Child, are being ignored."
Community safety approaches have worked well in the past, with reductions in children's offences, knife crime, binge drinking and anti-social behaviour, according to Together.
"This welcome approach under way in most parts of Scotland will be undermined if stop and search is not based on sound intelligence and professional judgement," the alliance said.
"Such pockets of poor practice where so many very young children are stopped will call into question the confidence of the community and, in particular, the children and young people.
"Our successful track record in reducing crime and anti-social behaviour would be at serious risk.
"We call on Police Scotland and its Police Authority to review urgently the current use of stop and search and any targets being set at a divisional level. Any review should involve children, young people and their communities."