No one has so far claimed responsibility for the attack.
As Russia held a series of rallies condemning terrorism, state television broadcast dramatic footage of police breaking into a St. Petersburg apartment and bringing out three men in handcuffs.
"While I entrust all those who are tragically deceased to the mercy of God, I express my spiritual closeness to their loved ones and to all those who are suffering because of this dramatic event" he said.
In a separate statementreleasedearlier on April 5, the committee said investigators had searched the home where Jalilov lived and had questioned about 40 witnesses. Jalilov is also accused of planting a second unexploded bomb hidden in a fire extinguisher that was discovered at a metro station two miles away from the blast.
President Vladimir Putin, whose hometown is Saint Petersburg, offered his own condolences and later placed a bouquet of red flowers at the entrance to one of the stations, Technological Institute.
The discovery of the explosives raises the possibility that a string of bomb attacks was being planned in the city involving a group of plotters.
"Time will be needed to find out how they found out to be there", he said. Officially, the Russian government says that all possibilities are still being investigated, despite Russia's general prosecutor opening a terrorism investigation. A high-speed train between Moscow and St. Petersburg was bombed in November, 2009, killing 26 and wounding over 100.
Three people have been arrested over suspected links to the suicide bomber who attacked St Petersburg's subway.
"Investigators have identified a male suspect who set off an explosive device inside a metro train in Saint Petersburg", Svetlana Petrenko, spokesperson of the Investigative Committee said in a statement."The suspect is Akbarzhon Dzhalilov, born in 1995".
Investigators said there was no evidence linking the six men to Monday's bombing.
While most Central Asian migrants in Russia have work permits or work illegally, thousands of them have received Russian citizenship in the past decades.
The impoverished, predominantly Muslim countries in Central Asia are seen as fertile ground for Islamic extremists, and many are believed to have joined the Islamic State group in Syria and Iraq. ISIS has previously said it would carry out terrorist attacks in Russian Federation.
Investigators believed the men were Dzalilov's accomplices, a source told the Interfax news agency. It is now unclear whether the suicide bomber is the same suspect from Kyrgyzstan named Akbarzhon Jalilov.
A suicide bomber was behind the attack that killed 14 people and left dozens wounded.