Krasikov, who was freed along with seven other Russian citizens on Thursday, had been serving a life sentence in Germany for assassinating a former Chechen rebel in a Berlin park.
In the run-up to the swap deal, the German Justice Ministry had sought an official opinion from the public prosecutor's office on whether Krasikov should be freed, the spokeswoman said.
The institution put forward arguments "in favour of continued enforcement" of Krasikov's sentence.
However, the ministry ultimately decided "the arguments against continued enforcement of the sentence" were more compelling.
"This is because further enforcement would have caused a risk of serious harm to Germany and its foreign and security policy interests," the spokeswoman said.
There were also "overriding public and humanitarian interests" including "protecting the lives, health and freedom" of German nationals and dissidents in prison in Russia, she said.
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Justice Minister Marco Buschmann on Thursday said the decision to free Krasikov had been "a particularly bitter concession".
"In order to give 16 people a new life in freedom, we have deported a convicted murderer to Russia," he said in a statement.
Chancellor Olaf Scholz acknowledged the decision to release Krasikov had been "difficult".
But speaking after welcoming the prisoners at Cologne airport, Scholz insisted the swap was "the right decision, and if you had any doubts, you will lose them after talking to those who are now free".
Krasikov, alias Vadim Sokolov, was found guilty of gunning down former Chechen separatist commander Zelimkhan Khangoshvili in broad daylight in a Berlin park in 2019.
He was convicted in December 2021, with Berlin judges concluding the killing had been ordered by Moscow.
The Kremlin at the time slammed what it called a "political" ruling, but Moscow on Friday confirmed that Krasikov was an operative with Russia's FSB security service.
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