He said the gunmen stormed Baanu around 8.30 pm (1930 GMT), shooting sporadically.
Baanu resident Aisami Ari who fled the attack to the state capital Maiduguri on Saturday, also confirmed the attack and the death toll.
A government official, who demanded anonymity, however put the death toll in Baanu at 56.
Kolo also said four people were killed in another attack by the Islamists in Karnuwa village on Saturday.
"They shot dead four people in the village, including the chief imam of the village, his son and two neighbours," he said.
Local resident Saleh Musa told AFP of a third attack on Hambagda on Sunday where they killed seven villagers and injured five others.
- Attackers on horses -
"The attackers arrived on horseback around 2:00 pm while people were praying in the mosque. They went straight to the mosque and opened fire on worshippers," said Musa who later fled to the nearby town of Askira Uba.
"They killed seven people, while five others were injured. I was late for the afternoon prayers and I was at home preparing to go to the mosque and join in the prayers when the attack happened."
Army spokesman in Maiduguri, Colonel Tukur Gusau, and Borno government spokesman Isa Umar Gusau said they could not immediately comment on the attacks.
Boko Haram has stepped up its attacks since Nigeria's new President Muhammadu Buhari was sworn in on May 29, vowing to crush the insurgency.
The wave of violence since the inauguration has claimed more than 1,000 lives, dealing a blow to a four-country offensive launched in February that had chalked up a number of victories against the hardline Islamists.
The extremists have carried out deadly ambushes across Nigeria's borders and in recent weeks suicide bombers, many of them women, have staged several attacks in Nigeria, Cameroon and Chad.