"At the moment we have 44 dead bodies and 47 others injured from the scenes of the two attacks," Mohammed Abdulsalam, from the National Emergency Management Agency (NEMA), said.
Earlier, police in Plateau state, of which Jos is the capital, said at least 18 people had lost their lives in Sunday night's attacks at a shopping complex and a site near a popular mosque.
Discrepancies in death tolls are not unusual in Nigeria. The police, military and government authorities previously downplayed death tolls in the Boko Haram insurgency.
There was no immediate claim of responsibility for the attacks but religiously divided Jos has been targeted before by the Islamist militants.
Plateau, which falls on the dividing line between Nigeria's mainly Christian south and mostly Muslim north, has also seen waves of sectarian violence that has killed thousands over the last decade.
Boko Haram stepped up its attacks in northern Nigeria since the inauguration of president Muhammadu Buhari on May 29, with a wave of raids, explosions and suicide bombings.
With the latest attacks, more than 500 people have been killed, according to news agency AFP.
On Sunday, a suicide bomber blew himself up inside a church in the city of Potiskum, in north-east Nigeria, killing five worshippers.
Last week, Islamist militants fighters raided a number of villages around the Lake Chad area, killing more than 150 worshippers as they prayed in mosques.