It was not immediately clear whether the hostages died at the hands of the attackers or during the rescue late on Sunday night in an affluent neighborhood of the capital.
The incident began when militants wearing suicide vests and armed with grenades attacked the Iraqi stock exchange at dusk Sunday before turning their attention to the nearby Our Lady of Deliverance church - one of Baghdad's main Catholic places of worship - taking about 120 Christians hostage.
Maj. Gen. Hussein Ali Kamal, the deputy interior minister, said 52 people were killed and 67 wounded, in the bloodbath. Officials said at least one priest and 10 policemen were among the dead. Many of the wounded were women.
A Christian member of parliament on Monday described the Iraqi rescue operation as "not professional," saying "it was a hasty action that prompted the terrorists to kill the worshippers."
"We have no clear picture yet whether the worshippers were killed by the security forces bullets or by terrorists, but what we know is that most of them were killed when the security forces started to storm the church," Younadem Kana said.
Video footage from an American drone that was overhead during the attack showed a black plume of smoke followed by flashes from inside the building before what appears to be soldiers going in. U.S. forces often supply air support to Iraqi forces conducting operations on the ground, feeding them video footage of what American drones see from the air.
The casualty information was confirmed by police and officials at hospitals where the dead and wounded were taken.
There were conflicting accounts about the number of attackers involved in the assault, with Baghdad military spokesman Maj. Gen. Qassim al-Moussawi saying Sunday night that security forces killed eight, while the U.S. military said between five and seven died.
Two police officers on the scene, however, say only three attackers were killed and another seven arrested afterward.
Outside the Syrian Catholic church Monday morning, Raed Hadi leaned against his car on top of which rested a casket holding the body of his cousin, who was killed in the siege. Hadi was waiting for the police to let him onto the church grounds to bury his relative. He railed against Iraqi authorities.
"It was a massacre in there and now they are cleaning it up," said Raed. "We Christians don't have enough protection. ... What shall I do now? Leave and ask for asylum?"
Police pushed back onlookers from around the church by erecting a barbed wire fence but residents and people from the Christian community claimed that it was too little, too late.
A cryptically worded statement posted late Sunday on a militant website allegedly by the Islamic State of Iraq appeared to claim responsibility for the attack. The group, which is linked to al-Qaida in Iraq, said it would "exterminate Iraqi Christians" if Muslim women in Egypt were not freed.
It specifically mentioned two women in Egypt that extremists maintain have converted to Islam and are being held against their will in Egypt. The two are wives of priests and are believed to have converted to Islam to leave their husbands since divorce is banned by Egypt's Coptic Church. One woman disappeared in 2004 and another in July.
Egypt's Christians had maintained they were kidnapped and staged rallies for their release. Both were later recovered by police, denied any conversions and were then spirited away to distant monasteries.
In the message, the militants claim the two are still Muslim and called upon the Vatican, which held a meeting earlier in October to discuss the fate of Christians in the Middle East, to release the women.
"We direct our speech to the Vatican and say that as you met with Christians of the Mideast a few days ago to support them and back them, now you have to pressure them to release our sisters, otherwise death will reach you all," the message said.
Iraqi Christians, who have been frequent targets for Sunni insurgents, have left in droves since the 2003 U.S.-led war. Catholics used to represent 2.89 percent of the population in 1980; by 2008 they were just 0.89 percent.
One Iraqi man who identified himself only as Abu Sami for security reasons, said his wife was inside the church during the attack. Although she was unharmed, he said he feared that the church siege signaled a new round of violence by militants against Iraq's Christian community.
"I expect the coming attacks will be worse in the future since the government is doing nothing to protect us. We are peaceful people and never harmed any of our fellow countrymen, so we do not understand the reasons behind such evil attacks," he said.
"Many Christians now believe that they do not have any hope in Iraq and the best thing to survive is to seek another country to live in," he said.
Associated Press writers Sinan Salaheddin in Baghdad and Sameer N. Yacoub in Amman, Jordan contributed to this report.