Wayne Mawson, an assistant chief constable at the single force, told MSPs today: "We should not be searching young children under the age of consent on a consensual basis. It has to stop. That's the message going forth that I will be putting out."
In last weekend's Sunday Herald Sunday Paul Hutcheon reported that babies as young as three months have been subjected to stop-and-search operations by officers from Scotland's national police force.
Police Scotland's own figures from its first nine months in operation reveal that 18 under-fives were searched for weapons, alcohol and drugs, with around half of the searches supposedly based on consent.
Liberal Democrat justice spokeswoman Alison McInnes said she was "shocked" by the revelation.
Stop and search was used heavily in Strathclyde and its extensive use has now been rolled out by Police Scotland.
The tactic is described as a key crime-fighting tool, but concerns have been expressed over its scale and use on young children.
A review by the Scottish Police Authority (SPA) found that 519,213 searches were carried out in the first nine months of Police Scotland. The SPA also revealed that 223 searches were undertaken on children aged nine and under, but no further breakdown was provided.
However, a database containing details of all stop and searches between April and December last year allows a complete picture to be revealed. Of the 223 searches, 207 were performed on six-, seven-, eight- and nine-year-olds.
According to the database, seven five-years-olds, two children aged four and one three-year-old were also searched.
Drilling down further, three two-year-olds, a toddler aged one, and two babies aged "0" were stopped.
Outwith the 223, the Sunday Herald also identified two searches where the age group given was "three months" and "eight months".
These two searches were undertaken in the Pentlands area of Edinburgh in April and September last year. One was a weapons search and the other related to alcohol.
The age of criminal responsibility is eight in Scotland.
It is understood that officers search young children if they believe parents have planted illicit items on them, such as a shoplifter hiding stolen goods in a pram.
In one case, it is believed CCTV footage showed an adult placing stolen goods on a child, while a five-year-old with a crossbow was searched.
Officers can either carry out statutory searches, when police have reasonable grounds of suspicion, or "non-legislative" searches, which are based on consent.
Ten of the 18 searches on under-fives were non-legislative, meaning that babies, toddlers and young children were recorded as consenting to the operation; 16 of the 18 searches failed to find anything.
Kath Murray, an Edinburgh University academic and an expert on stop and search, said: "Children as young as this are below the age of criminal responsibility and cannot possibly provide consent to be searched. We know this type of contact can distance children from the police, undermine trust and damage police-community relationships.
"The Scottish government also needs to engage with the awkward fact that most stop searches in Scotland lack statutory authority - and that the current policing approach appears to be out of kilter with an otherwise progressive and inclusive policy outlook on children and young people."
McInnes said: "The fact that the searches on children under five were recorded as 'consensual' is absurd. The Justice Secretary and First Minister do not seem to grasp that children as young as five cannot reasonably give consent."
Wayne Mawson, a Police Scotland assistant chief constable, said: "Searches of young children have resulted in the recovery of alcohol, drugs and knives which can and do cause harm and injury to children and adults and these searches are to keep these young children safe."