"Two died and several refugees were injured in the attack last night (Saturday)," a source with a humanitarian aid group said after the assault at the Tabareybarey camp housing some 10,000 Malian refugees near the town of Ayorou in western Niger.
Ayorou mayor Zakaria Oumarou also confirmed there had been an attack in late Saturday, but did not confirm the toll or give other details.
A similar attack two years ago on the Mangaize camp, home to 6,000 Malians, saw heavily armed men kill nine members of Niger's police and national security guard, according to authorities.
The UN refugee agency says more than 50,000 have sought refuge in Niger.
Despite a peace accord last year and a 2013 international military intervention, large tracts of Mali are still not controlled by domestic or foreign troops and remain subject to attacks by jihadist groups.