Saint Petersburg, Russia's second city, and Putin's hometown, was the scene of a deadly metro bombing in April and is set to host games during next year's football World Cup, raising fears of similar attacks.
"The suspect is being questioned," a spokeswoman for the Russian Investigative Committee, Svetlana Petrenko, said in a statement.
"The organiser and direct perpetrator who triggered an improvised explosive device on December 27 in a supermarket in Saint Petersburg was arrested during a special operation by the FSB", the security services added, according to Russian news agency Interfax.
The news agency quoted a source close to the case as saying the suspect was 35-year-old Dmitry Lukyanenko, a resident of Saint Petersburg and member of the nationalist "New Age" movement.
The homemade bomb had been placed in a locker at the supermarket in northwestern Saint Petersburg on Wednesday.
A pregnant women was among those injured in the blast, which was claimed by the ISIS. Eight people remain in hospital.
Putin's 2015 decision to begin a military intervention in Syria's conflict on the side of President Bashar al-Assad has made Russia a priority target for extremist groups.
'Killed On The Spot'
The city's subway was also targeted by a bomb attack in April that left 15 dead and dozens wounded, claimed by a little-known group linked to Al-Qaeda.
Earlier this month, the head of Russia's FSB security service, Alexander Bortnikov said that at least 4,500 Russians had left the country to fight with "terrorists" in the Middle East, North Africa and other regions.
Putin himself warned after Wednesday's bombing that armed criminals could be "liquidated on the spot".
"As you know, an act of terror took place in Saint Petersburg yesterday," Putin told officers who took part in Russia's Syria campaign during an awards ceremony.
He said he had ordered the nation's security services to "act decisively" and "liquidate bandits on the spot" if armed militants put up resistance.
Over the past 20 years Russia fought two wars with separatists in Chechnya, leading terrorists from the North Caucasus to frequently target Russians through suicide bombings and other attacks.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)
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