Next of kin have been asked for DNA samples to help identify the victims.
The Airbus A320-200, carrying 162 people from Surabaya to Singapore, disappeared on December 28 and remains were located in the sea on December 30.
The authorities say seven bodies have been retrieved, but bad weather is hampering further salvage efforts.
A public memorial will be held in Surabaya on Wednesday evening local time.
All New Year’s Eve celebrations have been cancelled.
On board the plane were 137 adult passengers, 17 children and one infant, along with two pilots and five crew.
It is not yet clear what happened to the plane but its last communication was a request from air traffic control to climb to avoid bad weather. The pilot did not respond when given permission.
A three-day search ended on December 30 when remains including aircraft parts, luggage and the bodies were found in the Karimata Strait, south-west of the town of Pangkalan Bun in the Indonesian part of Borneo.
The bodies were flown to Surabaya’s Juanda airport on Wednesday afternoon from a hospital in Pangkalan Bun, where they had been sent from the crash site.
Another five bodies are reported to be on board a ship on their way to a harbor near Pangkalan Bun.
Four of the seven bodies are male and three female, one of them a flight attendant.
Strong winds and high waves have slowed down the recovery of bodies and debris, with helicopters mostly grounded and divers prevented from searching the waters.
The weather is forecast to deteriorate further, with heavy rains until January 2, 2015.
Next of kin of passengers and crew have been asked for DNA samples to help identify the bodies when they come in.
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