The study claims Scotland is at risk of civil disorder similar to the Brixton riots of the 1980s and the 2011 London riots because of the "negative effect" they have on police relations with communities.
It reveals that use of the tactic in Scotland - under slightly different powers to those in England and Wales - is on average almost four times higher per person than for south of the Border. The Edinburgh University research found hundreds of children under 10 were being targeted, and more than 26,000 youngsters aged 14 and under agreed to the police checks voluntarily.
The academics also warn that officers may not be informing people of their right to refuse 'non- statutory' - non legally enforceable - searches, which have long been abandoned south of the Border, in breach of their human rights.
Earlier this week, Justice Secretary Kenny MacAskill and Police Scotland praised stop-searches for helping to produce a massive drop in violent crime.
About 500,000 people in Scotland have been subject to the initiative over the past nine months. Academic Kath Murray found in the report that the tactic was legally questionable, "unenforceable" and its deployment had increased by more than 300%.
Interviews with officers and analysis of data between 2005 and 2013 found that 76% of stop searches by the former Strathclyde force were consensual, but that such searches may breach human rights legislation and are not based on intelligence.
Ms Murray says in the report: "In practice, the use of non- statutory stop and search seems unlikely to meet the basic stand-ards required to secure consent. First, there is no duty on officers to inform a person of their right to refuse a non-statutory search. Secondly, age and the related capacity for understanding are not taken into account."
In some areas, the report finds "officers make extensive use of stop and search without reasonable suspicion". It goes on: "The troubled history of stop and search in England, from the Brixton riots through to the urban unrest in August 2011, has demonstrated the potential of search tactics to aggravate police-community relationships and to undermine police legitimacy."
It adds that Scotland should not be complacent and "public tolerance may reach a breaking point, leading to more open antagonism towards the police."
In the former Strathclyde force, stop searches increased by 312% - or 282,000 searches - between 2005 and 2010, the study found.
Dr Genevieve Lennon, lecturer in law at Dundee University, said: "It is highly questionable as to whether a 10-year-old can give legal consent but academics have also highlighted the fact that the power differential between the person stopped and the police is so great that any form of consent is likely to be based on acquiescence."
The study finds that, in 2010, the rate of stop-searches by Strathclyde was more than double that of the Met Police's, the force involved in the case of Mark Duggan, who was shot dead by police in 2011, sparking riots.
David O'Connor, president of the Association of Scottish Police Superintendents, said: "There should only be rare circum-stances where there will not be at least some suspicion or intelligence before a [consensual] search with consent will be carried out."
Police Scotland assistant chief constable Wayne Mawson said: "The use of stop and search, where it is targeted and intelligence led and used in the right place at the right time, is an effective and legal tactic."