An American NGO worker was abducted on Friday night from Abalak, northeast of Niger's capital Niamey before he was taken to Mali, a security source told AFP.
The source, who did not wish to be named said, "It is too early to determine the identity of the kidnappers, who have returned to Mali. The authorities have put the region on maximum alert".
"At least two people were killed during an exchange of gunfire" as the American was getting kidnapped.
"All roads to Mali are being monitored," the source said but did not give the identity of the victims.
A US state department spokesperson told AFP that they knew an American had been kidnapped but refused to comment.
This is the first time a US national has been kidnapped in the area, which known for abductions and armed violence. Since 2012, neighbouring Mali has seen attacks by militants when French-led military pushed them out.
Niger's President Mahamadou Issoufou had said last week, "To resolve the security problem in Mali is also to resolve the security problem in Niger."
Apart from the threat from Mali, Niger also faces attacks from Boko Haram, a Nigerian militant group.