Russia's FSB security service on Monday said it detained Kyrgyzstan-born Abror Azimov in a suburb of Moscow over the deadly April 3 blast that killed 14 people in Russia's second city.
The FSB alleged Mr Azimov was 'one of the organisers' of the attack and had 'carried out training' of the suspected 22-year-old suicide bomber Akbarjon Djalilov, who was born in Central Asian Kyrgyzstan.
At a court hearing Monday to formally arrest him, Mr Azimov admitted indirect "involvement" in the attack but denied organising it.
"I do not oppose being arrested. But I did not say that I was involved in the blast," Mr Azimov was quoted as saying by Russian news agencies.
"There was some involvement by me, but not direct. I was given an order. I did not understand that I was taking part in terrorist activity."
Russian agencies quoted investigators in court as saying that Mr Azimov had confessed to his role in preparing the attack during questioning.
The court later ordered Mr Azimov held in detention until June 3 as investigations continue.
Alleged bomber Djalilov is suspected of triggering a homemade explosive device that tore through a metro carriage as it was passing through a tunnel between stations.
Eight other men from ex-Soviet Central Asia have also been detained in Moscow and Saint Petersburg over the bombing.
No one has claimed responsibility for the attack but investigators are probing possible ties to ISIS, who have threatened to attack Russia in revenge for its intervention in Syria.