"In the region of Zinder, we have a few dozen people whom we arrested for checking. They are suspects," Kalla Moutari told AFP in an interview yesterday, adding that they were citizens of Niger.
The suspects were sent to an "anti-terrorist unit" in the capital Niamey, Moutari said.
Boko Haram launched a series of cross-border attacks in Niger's remote Diffa area on February 6.
The region is across the border from northeastern Nigeria, the Boko Haram stronghold.
He said some 10,000 people had fled the violence in Diffa to Zinder, and that the checkpoints allowed authorities "to intercept those who had infiltrated the displaced people.