Initially two persons died in the fire. Another person, who had sustained severe burn injuries, died in a hospital later.
Seven fire tenders were rushed to the spot at Christopher Road after the fire broke out at around 1 PM and the blaze was brought under control in about two hours, fire brigade officials said.
As the place was not an official gas cylinder godown, it was being ascertained how so many cylinders were stored there, the officials said.
Fire Services Minister Sovan Chatterjee, who is also the City Mayor, said an investigation was on to unearth how such a huge quantity of inflammable articles were stored illegally in the godown.
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"Steps will be taken as per law," the minister said.
Disaster Management Minister Javed Khan also said the police would take steps after investigation.
The entire area was cordoned off and traffic diverted.