Humza Yousaf has insisted it would be wrong for the Scottish Government to intervene after a rapist dodged jail.
Sean Hogg, 21, was handed a community payback order after being convicted, forcing him to complete 270 hours of unpaid work.
The sentence has prompted a political backlash - with the Tories urging the Scottish Government to urgently review sentencing guidelines.
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The guidance, which came into force early last year, said: "A custodial sentence should only be imposed on a young person when the court is satisfied that no other sentence is appropriate."
But final decisions are ultimately rendered by judges.
Hogg, from Hamilton, attacked his 13-year-old victim at Dalkeith Country Park, Midlothian, on various occasions between March and June 2018.
Speaking on a visit to Aberdeen today, the First Minister said: "I can understand the concern people have raised.
"But I also have to be quite careful. It was less than a week ago that I was in the Court of Session with the Lord President, who was rightly making the point that the judiciary is independent from government and ministers should not intervene in sentencing decisions.
"That's got to be a decision for the courts. I have also read comments in the press that the Crown may be considering an appeal to that sentence - but again, that's a decision for the Crown to make, independent of government."
Asked about the kind of message such a sentencing sent to victims, the First Minister added: "I can understand that.
"But also, this is one case, and the reason you're asking me about it - quite rightly so - is because it is the exception.
"In the overwhelming majority of cases, where an individual is convicted of rape, they end up with a custodial sentence.
"Again, I can understand why people are concerned about this particular case, but it is so important doesn't intervene or interfere in decisions made by our judiciary."
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In a letter to new Justice Secretary, Angela Constance, Tory MSP Jamie Greene said: “It is outrageous and appalling that such a despicable crime has not even been punished with a prison sentence and the public will rightly be wondering why this has happened in this case.
“The soft-touch approach to justice taken by the Scottish Government is at least partially to blame in this instance.”
He added: “I implore you to order a review of these sentencing guidelines as is the Scottish Ministers’ right under Section 7 of the 2010 Act with a view to scrapping the guidelines so that rapists and other serious criminals do not avoid prison in future just because they are under 25.
“As a new Justice Secretary you have the ability to change the direction of Scottish Government policy to get tough on serious criminals who commit such horrific crimes and I hope you will consider my request today.”
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