"Six attacks were carried out almost simultaneously on Sunday," the source said on condition of anonymity, saying the fighters were pushed back across the border by Cameroonian troops.
The latest raids came less than two weeks after 39 Boko Haram gunmen were reportedly killed in clashes with soldiers after crossing into Cameroon to mount attacks on three villages in the same region near Lake Chad.
The extremists reportedly suffered even heavier losses the previous week when 107 were killed in battles after another incursion, Cameroon's army claimed.
Most of the fighting took place around Kolofata and Fotokol, where the three civilians died. The two districts close to the Nigerian border have often been targeted by the extremists.
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Cameroon's Communications Minister Issa Tchiroma Bakary said the army had "inflicted heavy losses" on Boko Haram in recent weeks.
Boko Haram's five-year insurgency in Nigeria has left thousands dead, and the Islamists have occasionally carried out attacks over the border, including a raid earlier this year blamed on the group that saw 10 Chinese and 17 locals taken hostage.
UN regional chief Abdoulaye Bathily said today he was "extremely worried by the impact of Boko Haram on some countries in the region, notably Chad and Cameroon".
"We are alerting the Security Council... The countries concerned need support in their struggle with Boko Haram", Bathily added in statement.
Cameroon has deployed more than 1,000 soldiers in the extreme northeast of the country to counter the threat.