The suspect, who is reported to be from Kyrgyzstan, said he simply “followed” instructions, and “did not realize” what he was doing.
It came shortly after Abror Azimov’s lawyer told Russian media he had “fully confessed” to being behind the explosions.
A total of nine people have been detained over the April 3 attack.
Suicide bomber Akbarzhon Jalilov detonated a bomb between two subway stations.
More than 50 people were injured by the attack.
Russian security services previously said they believed Abror Azimov had trained Akbarzhon Jalilov, a Kyrgyz-born Russian, ahead of the bombing.
However, speaking in a Moscow court in on April 18, Abror Azimov said he “was involved, but not directly”.
He denied ever having confessed to organizing the attack.
“I did not understand that I was taking part in terrorist activity,” Abror Azimov said.
“I was given orders, and I only followed them.”
He told the court he was married, with one child, Vesti TV news reported.
Abror Azimov will be remanded in custody until June 3, while investigations continue.
Police had found Abror Azimov by examining Akbarzhon Jalilov’s phone contacts, Russian newspaper Kommersant said, citing sources.
Abror Azimov bought two new mobile phones and Sim cards on April 17, but gave away his location to security forces when he activated one of the cards, Kommersant added.
According to Russian media, Abror Azimov was born in Kyrgzstan in 1990, and moved to Russia in 2008. He reportedly became a Russian citizen in 2013.
The other eight people detained in connection with the attack – six in St Petersburg and two in Moscow – are also from Central Asia.
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