The eight-storey Rana Plaza factory building near Dhaka collapsed on 24 April with an unknown number inside.
The authorities say about 2,500 people were injured in the accident and 2,437 people were rescued.
The recovery operation is expected to finish on Friday. The rubble will then be shifted by bulldozers.
On Friday morning, officials said a total of 1,021 bodies had been recovered from the debris of the fallen factory building in Savar.
Many bodies were decomposed, but could be identified by mobile phones in their pockets or staff passes, Army Captain Shahnewaz Zakaria said, adding that “most [of the dead] are female garment workers”.
The authorities are taking DNA samples from the victims, which can be used in future compensation claims, AFP news agency reported.
Many bodies have been found beneath a collapsed staircase to which workers had fled when the collapse began, the Bangladesh Daily Star reported, quoting an army officer.
Bodies are being taken to a nearby school building where relatives of those still missing are waiting.
Correspondents say the silence is frequently broken by wailing as victims are identified by their families.
The Rana Plaza building had housed a number of garment factories.
A number of officials – including the building owner – have been arrested and charged with causing deaths by negligence.
Just a day before the collapse the building was briefly evacuated when cracks appeared in the walls. However, workers were later allowed back in.
The government has launched an inquiry and preliminary findings have blamed vibrations from four giant generators on the compound’s upper floors for triggering the collapse.
Protesters have taken to the streets calling for the death penalty for the owner, and garment workers have alleged that they were forced to work in the building despite the cracks in the walls.
Bangladesh has one of the largest garment industries in the world, and some of the clothes produced in the Rana Plaza building were made for Western retailers.
On Wednesday, Bangladesh announced a shut down of 18 garment factories for safety reasons, amid growing concerns over the issue of industrial safety across the country.
Earlier this week, a fire at another clothing factory in Dhaka killed at least eight people.
The fire engulfed the lower floors of the 11-storey building, sending out smoke and gas that suffocated victims as they ran down stairs, officials said.