Doctor Abd al-Razzaq al-Obaidi, the mortuary assistant manager, said on Wednesday the tally for June compared with the 1,375 bodies the mortuary received in May and 1,155 in April is the higest so far.
"June is the highest month in terms of receiving cases of violence since Samarra," he said.
Most of the bodies had gunshot wounds to the head, he said, a common feature of sectarian, execution-style killings.
Iraq's health, interior and defence ministries consistently provide lower figures than those released by the mortuary.
The figures show that the level of violence in Iraq has increased even after the killing in a US air strike on June 7 of Abu Musab al-Zarqawi, the leader of al-Qaeda in Iraq.
Zalmay Khalilzad, the US ambassador to Iraq, said on Tuesday the death of al-Zarqawi had not improved security.
Al-Zarqawi was blamed for a campaign of car bombs and suicide attacks that US and Iraqi officials said was aimed at starting civil war among Shia and Sunnis in Iraq.
Sectarian tension has been simmering since the attack on the Golden Mosque of Samarra, which US and Iraqi officials blamed on al-Qaeda.