The cause of the fire is still not known, but questions are being raised over the speed with which the fire was able to spread and the apparent failure of management to respond to the emergency.
Four people have been detained for questioning, including the head of the company that manages the shopping centre, according to the Investigative Committee.
"More bodies were discovered during the inspection of the scene and we confirm the death toll is at 48", deputy emergencies minister Vladlen Aksyonov said, according to Tass. Officials have confirmed that the blaze killed 64 people, including 41 children.
People gather to commemorate the victims of a shopping mall fire in Kemerovo on the day of national mourning in central Moscow, Russia March 28, 2018.
Mr Putin noted the highly combustible materials used to convert the centre from a Soviet-era confectionery factory and the absence of a functioning fire safety system, saying that investigators will track down all those responsible.
Wednesday's funerals - for some of the 27 identified victims - included those of a grandmother and two children. They were trapped there as the exits and one of the cinema halls had been locked.
Five people have been arrested in connection with the fire.
The reports didn't say if the victims died from burns or smoke inhalation.
"People, children came to relax", Putin told officials in Kemerovo after laying flowers at a makeshift memorial of flowers, stuffed children's toys and balloons near the gutted mall's facade.
The fire was extinguished on Monday morning after burning through the night.
Although the aftermath of the fire coincided with a deadline for many western states to announce political action against Russia after the nerve agent poisoning of a former Russian spy in the United Kingdom, many leaders issued messages of support to the grieving families of those killed in the blaze.
Kremlin spokesman Dmitry Peskov refused to comment yesterday on the regional authorities' actions, telling reporters that "Putin has said that it is hardly appropriate to issue hasty judgements".
A young man told Putin he was outraged that the doors were locked at the mall, effectively turning the premises into "gas chambers".
Putin met their representatives and promised justice after the investigation is over.