The Nigerian-based extremists frequently stage attacks in Cameroon, which is contributing to a regional force to wipe them out.
On Monday, four suicide bombers killed 35 people in the border town of Bodo.
In response, Cameroon said its soldiers crossed into Nigeria and killed 17 insurgents.
On Tuesday, The Associated Press reported that at least 40 civilians were killed in cross-border operations, quoting the deputy commander of a Nigerian civilian defense group who said he spoke to villagers in the Gwadale border community in northeast Nigeria.
Abba said his information came from relatives still trapped along the border.
Abba also quoted villagers who said Cameroonian troops on January 18 fired rocket-propelled grenades indiscriminately that killed a family of four in Nigeria, then shot and killed two elderly men.
Cameroon's Communications Minister Issa Tchiroma Bakary yesterday dismissed the AP report, saying Cameroonian troops were working "in perfect synergy" with Nigerian armed forces and have been trained to avoid human rights abuses.
Bakary said suicide attacks in northern Cameroon blamed on Boko Haram have killed 57 people and injured 70 since January 13.
It came days after diplomats said Nigeria refused requests from neighboring states to evacuate civilians and create a no-go zone along the border.
The White House said in October it would send up to 300 US troops to Cameroon to conduct airborne intelligence, surveillance and reconnaissance in the fight against Boko Haram.
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