According to the UN agency, an estimated 6,000 refugees have fled Nigeria's restive Borno State since 26 December, when clashes erupted between government troops and armed militias in Baga town, near the Chadian border.
Many of the refugees paddled across the lake to arrive in the Chadian village of Ngouboua, located on the shores of Lake Chad, 20 kilometres from the Nigerian border.
It takes three hours for the crossing.
Quoting what it called testimonies gathered by its teams, UNHCR said refugees are fleeing in fear of their lives after threats of retaliation and intimidation following militant attacks.
UNHCR and the Chadian authorities are carrying out registration and pre-screening of new arrivals to evaluate the needs for assistance.
An overwhelming majority of the new arrivals are women and children, with some 55 percent of them being minors according to initial UNHCR registration data.
“Efforts are also underway by UNHCR to move arriving refugees away from the border areas, due to security concerns and after a government request. So far, we have relocated some 4,200 refugees to the already existing Dar-es-Salam camp 45 kilometres away. The camps already hosts some 11,300 Nigerian refugees who have arrived since 2014” it said.
UNHCR said it is racing to provide timely shelter and other assistance to those arriving, including the most vulnerable.
New arrivals are hosted in collective shelters as UNHCR distribute relief items including blankets, mats and mosquito nets and hot meals.
Inside Nigeria, the same clashes have also forced tens of thousands of civilians to flee their homes, with more than 30,000 people arriving in Maiduguri, stretching even further beyond their limits the capacities of existing camps already hosting internally displaced people.
UNHCR is reiterating its call on the countries in the region to keep borders open for refugees fleeing insecurity in Nigeria.