"We are expecting a huge number of casualties," an Interior Ministry source told Reuters, saying there had been four blasts at churches in Baghdad and two in the northern city of Mosul.
Police in Mosul said they knew of just one church attack there.
The Vatican condemned the blasts - the first attacks on churches during the 15-month insurgency - echoing concerns among Iraqis that they aimed to inflame religious tensions.
In the deadliest attack, a suicide car bomber drove into the car park of a Chaldean church in southern Baghdad before detonating his vehicle, killing at least 12 people as worshippers left the building, witnesses said.
The US military has warned that guerrillas opposed to the presence of more 160,000 foreign troops may try to deepen divisions between the country's diverse religious communities in their campaign to destabilise Iraq.
"It is terrible and worrying because it is the first time that Christian churches are being targeted in Iraq," said Vatican deputy spokesman Father Ciro Benedettini.
A US military spokesman said three of the four attacks in Baghdad were known to be suicide car bombings.
An explosion at the Armenian church in Baghdad shattered stained glass windows and hurled chunks of hot metal. Another bomb exploded 15 minutes later at a nearby Assyrian church.
"Worshippers were inside the church and during the service a bomb went off," said Shakib Moussa Jibrail, a Christian.
An ambulance driver told Reuters that two people were killed in the explosion at the Assyrian church and several wounded.
US Colonel Mike Murray of the 1st Cavalry Division said at least 50 people had been wounded at the church, some seriously.
"Those are terrorist acts against the Iraqi people and against Iraq, and we're going to finish them (the terrorists)," Interior Minister Falah al-Naqib told reporters at the church.
In Mosul, officials said at least one person was killed in a blast at a church and 15 wounded.
There are about 800,000 Christians in Iraq, most of them in Baghdad. Several recent attacks have targeted alcohol sellers throughout Iraq, the majority of whom are Christians of either the Assyrian, Chaldean or Armenian denominations.
Christians account for about three percent of the population of Iraq, where attempts to provoke conflict have mainly focused on Sunnis and members of the Shia majority, who were oppressed by ousted dictator Saddam Hussein.
The US military says a computer disk captured earlier this year contained a letter from Abu Musab al-Zarqawi, a Jordanian militant allied to al Qaeda, calling for attacks on Iraqi Shias to try to spark sectarian conflict in Iraq.
In March, co-ordinated suicide bombings during a Shia religious ceremony killed more than 170 in Baghdad and Kerbala.
15 OTHERS KILLED At least 15 people were killed in other attacks across Iraq on Sunday including a car bomb blast outside police station just hours after US air strikes and clashes with insurgents in Fallujah.
At least four people died and scores were wounded in the northern city of Mosul when a driver hurtled towards a police station and crashed into concrete barriers where his car exploded.
The US military said five Iraqis were killed in the attack, including two policemen, while more than 40 others were wounded.
But an official at the morgue said only four bodies had been received after the blast ripped through the entrance of the police station and gutted nearby cars.
Medics at the two main hospitals in Mosul said a total of 51 police and civilians had been admitted with injuries.
Iraq's fledgling US-backed police and security forces have become frequent targets of insurgent attacks.
"A car bomb exploded at 8:05 (0405 GMT) in front of the police station in Summer, eastern Mosul," said local police Captain Nidam Mohammed.
In Baghdad, at least one Iraqi was killed and three were wounded, including a driver for the BBC, when a bomb narrowly missed a US convoy during the morning rush hour, the Al-Kindi hospital and the British news corporation said.
Later, two mortar rounds were fired on an Iraqi National Guard base, where at least 35 people were killed in a suicide car bombing on June 17.
In Fallujah, US air strikes and clashes on the ground between US marines and insurgents continued overnight in the anti-US bastion, west of Baghdad.
The city has proved one of the deadliest flash-points for US marines based in Iraq.
"We have 10 killed and 40 injured from both the bombardment and the earlier clashes," said Rafih al-Issawi, director of Fallujah's general hospital.
Many of the injured were women and children.
Insurgents attacked three military convoys, drawing return fire from US troops. Ensuing air strikes destroyed one building and an insurgent position, the US military said.
A US soldier was killed and two others wounded when a makeshift bomb exploded near the restive city of Samarra, north of Baghdad, the US military said.
The soldier died when their patrol was bombed at around 12:30 pm (0830 GMT), said a statement.
In Ramadi, the provincial capital of the restive Al-Anbar province, three civilians were wounded during a gunfight between police and insurgents, police and a doctor said.
A senior Iraqi government official confirmed on Sunday that four churches in Baghdad and two in the northern city of Mosul had been targeted in car bomb attacks and said he expected "huge casualties".
"We are expecting a huge number of casualties, but so far there are no specific numbers," said the official, who spoke on condition of anonymity.
As Beirut reported two Lebanese businessmen kidnapped in Iraq, New Delhi said abductors of seven truckers, comprising three Indians, three Kenyans and an Egyptian, had extended their deadline for starting to kill the captives by another 24 hours.
Two Turkish transport companies said they might suspend operations in Iraq to save the lives of two drivers taken hostage by Zarqawi's group.
Insurgent groups in Iraq have made hostage-taking a strategic tool to drive US allies out of the country. The Philippines withdrew its troops a month earlier than scheduled to save one of its nationals held hostage.