Legislation introduced at the end of last year allows jails to routinely photocopy prisoners’ mail instead of handing over the originals.
Dozens of academics have raised concerns this violates human rights, but Keith Brown, Scotland's justice secretary, said it had been welcomed by many inmates.
Prison bosses say there has been a shift in the past few years from drugs such as heroin and cannabis to so-called psychoactive substances, including synthetic cannabinoids.
These can be soaked or sprayed into paper before being posted to prisoners.
Between August 2020 and July last year, there were 8,869 mail items received in prisons which tested positive for an illicit substance.
Mr Brown said the use of psychoactive substances was "escalating".
He said there were five confirmed deaths involving etizolam, known as street valium, last year. This can be infused into paper, cards and clothing.
Rules which came into force on December 13 allow prison staff to photocopy mail in a bid to tackle the problem.
Mr Brown said there were early indications of a "significant decrease" in drug-related incidents and emergencies.
Giving evidence to Holyrood's criminal justice committee, he said: "There were 248 drug-taking incidents in October, 305 in November and 131 in December.
"There were 39 drug-related emergency escorts for the month of October, 37 in November and 15 in December."
However, an open letter signed by dozens of academics warned the new legislation was "an unjustified and disproportional infringement of human rights".
They said no specific evidence has been offered that mail is the primary cause of drug overdoses in prison, while the lack of consultation was "deeply concerning".
The experts said a review of drug deaths in 2020 and 2021 showed the majority were from substances prescribed within prisons and not new psychoactive substances.
In a separate letter, Sarah Armstrong, director of the Scottish Centre for Crime and Justice Research, said the new rules were not proportionate and created a significant risk of abuse of power.
Mr Brown acknowledged there were concerns around human rights.
However, he said the prison service must do all it can to protect staff and inmates.
Mr Brown said fears about an increase in mail in the run up to Christmas meant the legislation had been implemented faster than normal.
Confidential correspondence, such as court or medical letters, is not affected by the change.
Mr Brown said the attitude of prisoners was initially hostile, but became "much more supportive".
He said: "I think that's explained by the fact that the bullying and the medical fallout from the prevalence of these psychoactive substances in prisoners affects prisoners very directly.
"And they are in many cases very pleased to have this measure taken, not least because it leaves them less vulnerable to bullying to provide drugs for others."
However, Mr Brown later said there had been an increase in incidents of drugs being thrown over perimeter fences.
Teresa Medhurst, interim chief executive of the Scottish Prison Service, told MSPs staff were not allowed to read the mail before copying it.