DrugScope says that schools are breaching pupils' trust rather than helping them to make informed decisions about whether or not to use banned substances.
More than 100 schools are believed to regularly use dogs to identify drug-users. Kent, Staffordshire, the West Midlands, North Wales and Buckinghamshire have pioneered the approach.
A spokeswoman for DrugScope said: "It is breaking down trust relationships.
Drug awareness in schools should be all about giving children access to all the information they need - not chasing them out of school and driving drug use underground."
She said drug use was highest among truants who cannot be caught by the dogs. Some 60 per cent of truants say they have tried cannabis, compared with 15 per cent of pupils in school, according to a Mori poll in 2001.
The Secondary Heads Association urged schools to stick to the "tried and tested" measures of deterring drug use, such as relying on information from pupils.
John Dunford, general secretary of SHA, said: "The numbers we are talking about here are still a very small proportion of all schools."
But David Hart, general secretary of the National Association of Head Teachers, said: "I am certain we will see more schools using sniffer dogs - they are seen by many as an easier deterrent than drug-testing."
Two years ago, dogs were used on more than 3,000 pupils in 10 Kent schools and 62 young people were found to have had contact with cannabis.
Grosvenor International Services, an Oxfordshire-based security company, usually provides sniffer dogs for nightclubs but is now doing a lucrative trade with schools.
John Franklin-Webb, director of the firm, said: "Since we have been going into schools, there has been a reduction in the number of children bringing drugs in."
Some schools have used dogs to show pupils how police handlers work. But in one case last week, the idea backfired on pupils. At Ysgol Clywedog in Wrexham, visiting police dogs sniffed out six children who were carrying cannabis. The children were later cautioned by police.
The Department for Education and Skills warned earlier this year that dogs should be used with "extreme caution".