"The investigation identified the man who set off the bomb in the carriage of the Saint Petersburg metro". The authorities had not yet decided whether to press charges against the detainees, the statement said, according to Radio Free Europe website.
Authorities say there is no evidence those suspects, from former Soviet Central Asia, are connected to the bomb attack.
Russia's health minister raised the death toll to 14, including the bomber.
The City Hall said there were several foreign nationals among those killed and injured, but would not offer detail.
No claim of responsibility has been made for the Monday afternoon attack, which came while President Vladimir Putin was visiting the city, Russia's second-biggest and Putin's hometown.
Investigators suspect he was linked to radical Islamist groups and carried his improvised device in a backpack.
It was unclear if those detained at the site of Thursday's bomb scare were the suspected accomplices identified by the investigative committee. "The best confirmation of this are the recent tragic events in St. Petersburg", Putin said at the council of heads of the CIS security and intelligence agencies.
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Earlier state media reports quoted law enforcement sources saying the device had been hidden in a fire extinguisher and was larger than the one that exploded.
Train driver Alexander Kaverin continued to the next station after hearing the blast, a decision that aided evacuation efforts and helped save many lives.
The subway system in St. Petersburg, a city of 5 million that typically is crowded during peak commute hours, looked nearly deserted on Tuesday as many residents opted for buses.
The six detained were accused of recruiting "mostly immigrants from the republics of Central Asia to commit crimes of a terrorist nature and involvement in the activities of terrorist organizations banned in Russian Federation", including the so-called Islamic State, the statement said.
However, the man knew little and they tried to learn more by tapping phones of his contacts, the newspaper said.
Suicide bomber Dzhalilov was radicalised just two months ago on a trip to his native Kyrgyzstan when he said goodbye to his parents ahead of the St Petersburg train massacre. While attacks against police regularly occur in Russia's Caucasus, they are much rarer in other regions.
Russian Federation has always been battling an Islamist insurgency in its volatile Caucasus region and has suffered a string of bloody terror attacks over the years.