It comes a day after a bomb killed 14 people in the subway system of the Russian city, the hometown of President Vladimir Putin.
The Sennaya Square station in the city centre was cordoned off on Tuesday, and commuters were told via a PA announcement that three more stations have also been closed down.
Later updates said the stations had since re-opened.
Earlier on Tuesday Russia's health minister, Veronika Skvortsova, said the death toll had risen to 14. Forty-nine people are still in hospital.
And Kyrgyzstan's State Committee for National Security said in a statement it believed one suspect behind the bombing was a Kyrgyz-born Russian citizen it identified as Akbarzhon Dzhalilov.
Interfax news agency said authorities believed the 23-year-old suspect was linked to terrorist groups.
Russia's state investigative committee said the bomb may have been detonated by a man whose body parts were found in one of the train carriages. It declined to give the man's name, in contrast with its Kyrgyz counterpart.
"It has been ascertained that an explosive device could have been detonated by a man, fragments of whose body were found in the third carriage of the train," the committee, which has sweeping powers, said in a statement.
"The man has been identified but his identity will not be disclosed for now in the interests of the investigation," the statement added.
Putin said authorities were investigating the possibility terrorism was the motive for the bombing.
His spokesman, Dmitry Peskov, told reporters on Tuesday the fact the Russian president was in the city when the bomb went off, though several dozen miles away from where he was hosting talks, "makes one pause" and is "something for the intelligence agencies to analyse."
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4 April 2017 - 13:34
News ID: 821837
(AhlulBayt News Agency) - Emergency officials have closed four St Petersburg subway stations following a new bomb threat.