The pre-dawn attack left four civilians and one soldier dead and most of the village of Ngouboua torched before the jihadists were pushed back, the source said on condition of anonymity.
The attackers struck after crossing the lake from Baga, Nigeria to Ngouboua in Chad in large canoes.
Two-thirds of Ngouboua, where around 7,000 Nigerian refugees have sought refuge from the jihadists attacks, was torched in the onslaught.
Boko Haram has carried out several cross-border attacks on neighbours of Nigeria who have launched a regional operation to combat the group.
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