In one attack, gunmen disguised as soldiers fired on a crowd in a church compound, local MP Peter Biye said.
He said he had warned the army that the area was at risk after troops stationed nearby were withdrawn three months ago.
The latest attacks come as the army denied that several generals had been found guilty of aiding the militants.
Nigerian media reported on Tuesday that 10 generals and five other senior military officers had been tried before a court martial for supplying arms and information to the Islamist militant group.
However, a military spokesman called the reports "falsehoods".
This contradicted Interior Minister Abba Moro who in a BBC interview on Tuesday said it was "good news" that the army had identified soldiers who were undermining the fight against the insurgents, and that it sent a strong message to other serving officers.
Boko Haram has waged an increasingly bloody insurgency since 2009 in an attempt to create an Islamic state in Nigeria.
The BBC's Will Ross in Nigeria says the attacks on six villages over the last few days have been near the Mandara Mountains - a known Boko Haram hideout by the border with Cameroon.
Residents who managed to flee Attagara said that their village church first came under attack on Sunday when reportedly 20 people died.
Villagers retaliated and some militants were allegedly killed.
This seemed to prompt a revenge attack on Tuesday when militants dressed as soldiers pretended they had come to protect the village, Mr Biye said.
"They came in mass in military uniform with about 200 motorcyclesâ€¦ they said they came to rescue them [and] they should not run away," he told the BBC's Newsday programme.
Villagers were urged to come to the church, and people gathered believing it was the military, the MP said.
"They surrounded them - they started shooting them," Mr Biye said, adding that the gunmen then burnt many buildings.
Those who had fled into nearby hills reported seeing many dead bodies, he said.
When troops were based in nearby Chinene village, the area was calm but since their withdrawal three months ago the area had become the insurgents' "base", Mr Biye said.
Nigeria's government has been facing growing pressure both at home and abroad to do more to tackle the group and bring about the release of more than 200 schoolgirls kidnapped by the group in April.
Nigerian President Goodluck Jonathan declared a state of emergency in May 2013 in the three northern states where Boko Haram is most active - Borno, Adamawa and Yobe.
Boko Haram retaliated by stepping up its bombing campaign in cities and launching mass attacks on small towns and villages.
Correspondents says since the kidnapping of the girls, the attacks have become an almost daily occurrence.
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Suspected Boko Haram militants have killed dozens of villagers in fresh attacks in Borno state in north-eastern Nigeria, the BBC has learnt.