A senior army official also said that a list of 149 people still missing had been compiled from relatives.
Thousands marched in May Day parades in Dhaka on Wednesday, demanding the death penalty for the building’s owner.
The Rana Plaza, which housed five factories, collapsed last Wednesday – the nation’s worst industrial disaster.
Police officials confirmed that 399 bodies had been pulled from the wreckage, while another three people had died in hospital.
The army general said the list of the missing had been drawn up by local officials and was confirmed by Dhaka district administrator Zillur Rahman Chowdhury.
Earlier estimates had put the figure far higher but this may have been as a result of duplications. Some 2,500 people were injured.
‘Hang the killers’
The building was turned into 600 tons of rubble in the disaster, about 350 tons of which has now been cleared.
The number of people at the main Dhaka protest was put at about 20,000, with other demonstrations in separate parts of the capital and in other cities.
Some in Dhaka held banners with the words: “Hang the killers, Hang the Factory Owners”.
One protester blared through a loudspeaker: “My brother has died. My sister has died. Their blood will not be valueless.”
Kamrul Anam, of the Bangladesh Textile and Garments Workers League, said the building collapse was murder, telling AFP: “We want the severest punishment possible for those responsible for this tragedy.”
The protesters also demanded better working conditions.
Garment worker Mongidul Islam Rana told Associated Press: “We want regular salaries, raises and absolutely we want better safety in our factories.”
The Rana Plaza’s owner, Mohammed Sohel Rana, is in police custody.
A total of eight people have been arrested, including factory owners and engineers, and they have been accused of negligence.
Cracks had appeared in Rana Plaza, in the Savar district, the day before the collapse but the staff were reportedly told to continue work.
Many factories have been closed since the disaster, with regular street protests.
On Tuesday night, Prime Minister Sheikh Hasina urged people to return to work.
She said in parliament: “I would like to tell the workers to keep their head cool, keep mills and factories operative, otherwise you will end up losing your jobs.”
Meanwhile the European Union said it was considering “appropriate action” to encourage improvements in working conditions in Bangladesh factories.
It said its actions may include the use of its trade preference system, which gives Bangladesh duty- and quota-free access to EU markets.
Bangladesh has one of the largest garment industries in the world, with the sector making up almost 80% of the country’s annual exports.
The industry provides employment to about four million people.
However, it has faced criticism over low pay and limited rights given to workers, and for the often dangerous working conditions in factories.