"Some started heading back by themselves a couple of days ago and this morning a voluntary return operation" was launched, said Moussa Douma, mayor of the town of Ayorou - where thousands of displaced women and children had taken refuge.
"Armed forces were deployed" to the troubled area ahead of their return "to guarantee security," he said.
The displaced people live on remote islands on the Niger River in Tillaberi, a region that has borne the brunt of a jihadist insurgency that swept in from neighboring Mali in 2015.
The militants have inflamed tensions between two communities - riverside farmers from the Djerma community and nomadic Fulani herders - who usually live peacefully side-by-side, according to a local journalist.
The exodus began after an attack on May 6 in which four people in Dessa district were killed and a fifth wounded, according to the state-run Voix du Sahel (Voice of the Sahel) radio station.
The government is providing aid in the form of fuel for their boats, as well as food and shelters, Douma said.
On Sunday, Interior Minister Hamadou Adamou Souley gave the first official acknowledgement about the violence there.
"There was a crisis and the situation caused several people to leave their districts for safer places," he said on state TV, adding "Calm and peace have returned."
Niger is also struggling in the southeast with jihadist insurgents from Nigeria.
The impoverished Sahel state is supported by a number of western countries, including France and the United States, which both have military bases there.
Niger's Displaced Coming Back
FILE: People displaced due to jihadist violence attend a meeting of the President of Niger, Mohamed Bazoum (not seen), on June 2, 2022 in the city of Makalondi, southwestern Niger, the area since 2017 of bloody attacks attributed to Islamic State in the Greater Sahara (ETGS).
NIAMEY - More than 18,000 people who have fled conflict in jihadist-hit western Niger are being given help to return as security for the area is beefed up, officials told AFP on Monday.