The region which borders Mali has faced a series of recent jihadist incursions.
"There was a new attack. Twelve gendarmes were killed. We have launched search operations," Mohamed Bazoum told AFP.
The dawn raid happened in the town of Ayorou in the Tillaberi region, 200 kilometres northwest of the capital Niamey.
A security source said the attackers arrived in five vehicles and fled when military reinforcements arrived. Villagers saw them leave carrying bodies.
On October 4 four US and four Niger soldiers were killed in what Niamey called a "terrorist attack" that confirmed the little-known presence of US troops in the turbulent area as part of a counter-terrorism operation.
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But Tallaberi has become increasingly unstable due to numerous deadly attacks attributed to jihadist groups who regularly target army positions and refugee camps.
In mid-May unidentified assailants attacked the same Ayorou gendarmerie without causing any casualties.
Yesterday, parliament agreed a three-month extension of the state of emergency in western Niger because of the "continuing threat" of armed groups.
The UN said this week it has documented "at least 46 attacks" in Niger since February 2016.
In June, Niger set up an operation of 245 men to fight against jihadists but has not yet reported on its progress.
Malian foreign affairs minister Abdoulaye Diop stressed in front of the UN Security Council in New York this month the urgent need to help a new international security force get off the ground.
The so-called "G5 Sahel" coalition of Burkina Faso, Chad, Mali, Mauritania and Niger -- countries that have been badly hit by jihadist attacks but whose military resources are thin -- have pledged to fight terror but face funding problems.
Entire zones still escape the control of Malian and foreign forces, despite a military intervention by France in 2013.