"A Kia-branded car drove into the church premises ... then detonated the bomb" with the driver still inside, a military officer told the Reuters news agency, asking not to be named. The first blast ocurred at around 1145GMT.
"Then an ash-coloured Toyota Camry drove in and exploded while people came to help after the first bomb. Most people died from the second blast."
Nigeria's National Emergency Agency confirmed there had been an explosion inside the barracks and said it was "likely at a worship centre".
"I saw five bodies and scores injured," a second officer told Reuters. The death toll has not yet been officially confirmed.
"There was a blast today in a church inside the military barracks in Jaji," military spokesman Colonel Sani Usman told the AFP news agency.
"It happened after the church service."
But army spokesman Bola Koleoso disagreed with earlier accounts and said a bus drove into the side of the St Andrew Military Protestant Church and exploded at around 1105GMT, five minutes after a service had started.
There are different accounts of the incident, explained Al Jazeera's Ahmed Idris.
"First there was a report that a huge bomb blast took place, injuring some people and killing some, probably at least five people - but this has not been independently confirmed," he reported from Nigerian capital Abuja.
"But there are other stories that say that one bomb went off, and as people gathered to see what happened, a second device went off, injuring several, and killing five people at the church.
"There is no claim of responsiblilty yet, but this comes less than 48 hours after the military issued a statement declaring at least 19 top commanders of Boko Haram 'wanted'. There was a bounty of 50 million Naira ($318,000) on the leader of the group, a man named Abubakar Shekau, and 18 other lieutenants of the group.
"This is also coming on the same day that gunmen in the northwestern state of Sokoto attacked a police station, and took away some guns and ammunition. It's not clear at the moment who carried out the attack, but all pointers, all suspicions are directed at Boko Haram. the group has been targeting churches and other military installations across northern Nigeria in the past two years."
Al Jazeera's Yvonne Ndege, reporting from Lagos, said the bombing "could be a way of showing the Nigerian security services that [Boko Haram] is still strong and can still perpetrate these acts of violence".
"Obviously there will be an investigation by the military, police and security services, but it is very difficult to see what strategy the government can impose to deal with these sort of attacks," she said.
Jaji is some 30 kilometres from the state capital, Kaduna City. The state in northern Nigeria has been the target of several bomb attacks this year, including some at churches. Previous attacks have been claimed by Boko Haram, an armed group which has killed hundreds in its insurgency.
Boko Haram has claimed to be seeking an Islamic state in Nigeria, Africa's largest oil producer.
However, its demands have repeatedly shifted and it is believed to include various factions with differing aims, in addition to imitators and criminal gangs that carry out violence while posing as members of the group.