More than 60 people gathered outside the building on Tuesday with empty coffins stuffed with plastic to collect the bodies of relatives killed in the fighting since Wednesday's bombing.
Women beat their chests in a traditional sign of grief and wailed for their dead relatives.
Others clustered around two computers, looking through pictures to find missing relatives.
More than 300 Iraqis were killed around Baghdad alone in the sectarian violence triggered by the bombing of the Shia shrine.
Abd al-Razzak al-Ubaidi, the acting director of the central mortuary, told Reuters his unit alone had received 240 bodies between the attack on Wednesday and Sunday, nearly all victims of the violence.
Not all Iraqi deaths in Baghdad are recorded in the central mortuary, but it sees a high proportion of those who die violently. Other deaths are more typically registered at hospitals.
Qais Hasan, a mortuary duty manager, said 85 more bodies were delivered to the mortuary in the last 24 hours, taking the total to 309, the vast majority of them victims of political violence.
He dismissed a report that mortuary officials had taken in 1300 bodies since the shrine incident in Samarra north of Baghdad.
Mortuary data indicated that the figures were well above the average number of corpses received in six days.
Al-Ubaidi's data suggested that 10,080 were killed in Baghdad in 2005 of which 80% suffered violent deaths. The killings in the city were 70% above average for the past six days.
The attack on the Golden Mosque in the town of Samarra north of Baghdad set off sectarian reprisals and plunged Iraq into its gravest crisis since a US-led invasion toppled Saddam Hussein in 2003.
Iraqi and US officials disputed police tallies of deaths and said on Saturday only 119 had died across Iraq by then.
Major Falah al-Muhammadawi, an official at the Interior Ministry, said only 216 bodies could be confirmed since the al-Askari shrine was destroyed in Samarra.
But its information is based on death certificates which can take days to process.
Most of the victims had been shot, but some were strangled, he said.
The bodies brought in since Monday died of natural causes.
Sectarian attacks spread rapidly from Samarra to Baghdad and Shia area in southern Iraq.
An extended curfew and appeals by religious and political leaders curbed the worst of the violence, but sporadic attacks continued into this week.