Abror Azimov, who is reported to be from Kyrgyzstan, said he simply "followed" instructions, and "did not realise" what he was doing.
It came shortly after his lawyer told Russian media he had "fully confessed" to being behind the blasts.
A total of nine people have been detained over the 3 April attack.
Suicide bomber Akbarzhon Jalilov detonated a bomb between two metro stations.
More than 50 people were injured by the blast.
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Russian security services previously said they believed Abror Azimov had trained Jalilov, a Kyrgyz-born Russian, ahead of the bombing.
However, speaking in a Moscow court in on Tuesday, Mr Azimov said he "was involved, but not directly".
He denied ever having confessed to organising the attack.
"I did not understand that I was taking part in terrorist activity," he said.
"I was given orders, and I only followed them."
He told the court he was married, with one child, Vesti TV news reported.
He will be remanded in custody until 3 June, while investigations continue.
Police had found Mr Azimov by examining Jalilov's phone contacts, Russian newspaper Kommersant said, citing sources.
Mr Azimov bought two new mobile phones and Sim cards on Monday, but gave away his location to security forces when he activated one of the cards, Kommersant added.
According to Russian media, Mr 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.
A suspect arrested in Russia on Monday has denied he was behind the St Petersburg metro bombing that killed 14 people, Russian media say.