In the first blast, 27 people were killed and many more injured when St Theresa's Church in Madalla near capital Abuja was targeted. The spokesman for radical sect Boko Haram, Abu Qaqa claimed responsibility for the attacks.
The death toll rose to 39 as another church bombing and two suicide attacks were witnessed in other northern cities.
The explosion at St. Thesera's Catholic occurred after a Mass to celebrate Christmas while the second church bombing took place in a Mountain of Fire church in central city of Jos where constant clashes have taken place between Muslims and Christians.
Police in cities of Damaturu in Yobe state and Maiduguri in Borno state today said the number of wounded are still being counted as a suicide bomber attacked the two restive cities.
The carnage in Madalla left at least 17 cars damaged by the bomb which killed those who queued up to drive or board commercial vehicles to their homes.
The increase in number of deaths from an initial 25 came as more died in hospitals where they were taken to for medical attention.
"The owners of these vehicles queued up to drive home after the early morning mass where the message of love, peace and joy was delivered to herald the Feast of Nativity. Sadly, what we met was this ugly situation," the pastor of the church, Rev. Fr. Isaac Achi told PTI.
One of the victims was found on the roof of the church while several dead bodies were littered in gutters and other parts of the premises.
"The victims have been moved to different hospitals but at St. Lucas hospital, nine of my parishioners were recorded dead. At Diamond Hospital, a little baby of 5 years who was injured could not locate his parents," Achi said, adding that some other victims were commercial vehicle operators who came in to pick passengers.
Angry youths gathered to protest after the attack, but were dispersed by the police.
The explosion in Jos killed a police officer and while three vehicles were destroyed.
"The officers of Search and Rescue Team of NEMA in collaboration with stakeholders have evacuated at least 10 dead bodies from the explosion scene at Madalla to hospitals," Yushua Shuaib, the spokesman for the National Emergency Management Agency told PTI.
According to him, the evacuation exercise was still going on and the military was also involved in the rescue operation.
In Yobe state, police commissioner Tanko Lawan said a suicide attacker targeted the headquarters of the oil rich African country's secret police, State Security Service (SSS).
Boko Haram sect, which wants to install an Islamic government, has been waging war with the state in its quest to fulfil its ambition.
More than 100 people mostly their members were killed last week when the army engaged them in gun battles in Damaturu, Maiduguri and Potiskum.
Nigeria has both Muslims and Christians, the two communities having an equal share in the country's population of 150 million.
Boko Haram also claimed responsibility for several bombings and shootings in the north and capital city of Abuja.
A suicide bomb attack by the group at the United Nations headquarters in July killed 26 persons and injured more than 70.
The group’s leader, Muhammed Yusuf was killed in 2006 during an insurrection which claimed more than 800 lives.