Sweden's Schools Inspectorate previously refused to grant the school permission for the tests and has condemned the move. The head of Brinellgymnasiet, Jan Andersson, told Swedish Radio News that random testing is justified and that many pupils had already agreed to participate.
It is unclear how students will be called for the tests. One option being considered involves sending text messages to students' mobile phones, in order to avoid stigmatising those selected.
According to the Swedish Schools Inspectorate, it is illegal to carry out obligatory drug tests and students may feel forced into taking voluntary tests.
"I am very suprised that the local authority has not accepted our decision," said Ann-marie Begler, director of the Schools Inspectorate.
"We are appointed by the government to interpret and apply the law in schools and the local authority has clearly not accepted that. I think it's incredible"