The officials have said they were investigating suspected accomplices of the man behind this week's deadly metro bombing.
There was no immediate claim of responsibility or any information linking the suicide bomber to Islamist extremists.
The suspected bomber was identified as Akbarzhon Dzhalilov, 22, Russian authorities said on Tuesday.
RIA Novosti news agency and some Kyrgyz media outlets reported that Dzhalilov was born in Kyrgyzstan and attained Russian citizenship.
Authorities have also beefed up security across major cities, with sniffer dogs and bag checks at several metro stations in Moscow.
Another bomb, hidden in a bag, was found and de-activated at another St. Petersburg station just half an hour before the blast.
"I told (Putin) that terrorism is unforgivable, no matter the reason, and I resolutely condemn it", Abe said. The Central Asian men were accused of recruiting other men from the region to join the Islamic state and other terror groups.
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St. Petersburg was already on high alert after an explosion between two subway stations Monday killed 14 people and injured dozens others.
St. Petersburg is home to a large diaspora of people from Kyrgyzstan and other ex-Soviet republics in Central Asia, who flee poverty and unemployment in their home countries for jobs in Russian Federation.
One of those stations was closed by a bomb threat Tuesday and again on Wednesday as officials checked for anything suspicious.
Council members "expressed their deep sympathy and condolences to the victims of this heinous act of terrorism and to their families, and to the people and to the government of the Russian Federation", a statement said.
Young people hold candles as they gather to honor the memory of the victims of subway bombing on Marsovo Polye in St. Petersburg, Russia, Wednesday, April 5, 2017. "The recent tragic events in St. Petersburg are the best confirmation of this", Putin said at the meeting in Moscow. Earlier on Thursday, mourning continued in St Petersburg as the jittery city laid to rest the 14 people killed in the attack.
In the wake of the attack Putin spoke to a string of leaders around the globe-including holding only his second phone call with US President Donald Trump overnight.