The exodus notably follows an attack on Saturday night in which four people in the district of Dessa were killed and a fifth wounded, the Voix du Sahel (Voice of the Sahel) said.
Women and children fleeing the remote islands have sought safety in Ayorou, a town 200 kilometers from the Nigerien capital, Niamey, it said.
The station blamed "atrocities... (by) armed bandits" - a term typically used for suspected jihadists.
But local sources said there had been a surge in ethnic violence in the area that had been fueled by jihadists.
Inhabitants said that in late April, clashes broke out between riverside farmers from the Djerma community and nomadic Fulani herders, leaving several dead. The two groups usually live peacefully side by side.
A local journalist said jihadists were the cause of the violence, inflaming tensions by killing villagers, stealing cattle and demanding a "tax" from inhabitants.
An elected official in Ayorou said that "before the clashes, armed men on motorbikes gave an ultimatum to the farmers, telling them to leave their homes."
The area lies in the western region of Tillaberi, which is grappling with a jihadist insurgency that swept in from neighbouring Mali in 2015.
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.
Thousands Flee Niger Jihadi Attacks
FILE: A Niger Army soldier stands guard, as supporters wait for the arrival of Niger President Mohamed Bazoum, in Sara-Koira on September 11, 2021. - In recent months, attacks, often by perpetrators on motorcycles, have intensified against civilians in this heavily forested area.
NIAMEY - More than 13,000 women and children have fled islands on the Niger River in western Niger following "atrocities" carried out by jihadists, state radio said on Tuesday.