Questions have been raised about the likely effectiveness of random drug testing in schools.
The school has the support of its local education authority
Random testing has started at Abbey School in Kent, thought to be the first state school to have tried it.
It argues the tests give children an excuse to say "no" to drugs. Anti-drugs charities say they doubt the deterrent effectiveness of the tests.
And because prior consent is needed, only those who know they have done nothing wrong will take part, they say.
First samples taken
Each week at the Abbey School, in Faversham, a randomly-chosen group of pupils will be tested.
Mouth swabs were taken from at least 10 on Wednesday from among the school's 960 girls and boys aged 11 to 19.
Their samples were sent off to a laboratory to be examined, with results expected in three days' time.
The head teacher, Peter Walker, said children were looking for an excuse to say no to drugs, against peer pressure, and the scheme would give them that excuse.
"One of the difficulties we have got in our society is that the government has tried so hard and so much to try to improve levels of prevention, yet we are not meeting with enough success," Mr Walker said.
Paul Carter, Kent council cabinet member for education, said random drug testing was fraught with legal problems so the council had issued guidance.
"I believe the tests will be a strong deterrent to youngsters dabbling in drugs at parties on the weekend," he said.
There were differences of opinion among students arriving on Wednesday.
One 16-year-old said his parents had refused permission for him to take part.
"I don't agree with it. It's an invasion of privacy. It should be up to your mum and dad to sort this kind of thing out," he said.
A 14-year-old girl said she supported the measure because it could reduce drug-taking.
"I don't have a problem with taking a test. It depends if you've got anything to hide," she added.
But this is one of the issues flagged up by civil rights group Liberty.
Spokesman Barry Hugill said the effect might be to criminalise innocent children.
"If they refuse, the implication is obvious: you've got something to hide."
Charities are sceptical. Drugscope chief executive Martin Barnes said there was no proof random drugs tests had a deterrent effect.
"Testing risks driving drug use further underground and could result in an increase in truancies and exclusions," he said.
Steve Rolles of the Transform Drug Policy Foundation said "intrusive" random tests were not needed to give children an excuse to say "no". They needed accurate information.
But also such tests were only for illegal drugs - whereas alcohol, tobacco and solvents were far more harmful, he said.
Former government drugs adviser Keith Hellawell said that if those tested had consented in advance, and again at the time of the test, then clearly they knew there would not be drugs in their systems.
There had to be some penalty for failing to take a test, he argued.
Concerns have also been raised in part because the scheme is being sponsored by a tabloid newspaper and the drug test health firm.
The Shadow Home Secretary, David Davis, said Conservatives would "support, encourage and accelerate" random drug tests.