Witnesses in Abalak described the abductors forcing the aid worker to strip down to his undergarments before putting him in their four-wheel drive vehicle, a government source told CNN on condition of anonymity.
The source said removing clothes from hostages was a usual practice of terrorist groups trying to avoid being tracked.
Authorities are taking all necessary measures to locate the American and his abductors, including imposing a heavy military presence between Abalak and the border with Mali, said the source, who was not authorized to speak publicly.
The assailants stormed the aid worker's home, the interior ministry said. The slain guard was the aid worker's bodyguard, according to the source.
The American had been working with the locally based aid organization JEMED, said a spokesman for Youth With a Mission
, which is affiliated with the group.
The aid worker has 29 years' experience in Niger, spokesman Pete Thompson told CNN.
"It is not known where he has been taken and no group has yet claimed responsibility for his abduction. His family have been informed and the US government is tracking the situation. Out of respect for his family no name is being released at this stage," he said.
State Department response
The kidnapping marked the first time a foreigner had been abducted in the area, the government source said. There has been no claim of responsibility so far.
The US State Department said it was aware of reports of the kidnapping.
"The safety and security of US citizens overseas is among our highest priorities. We have no further information to offer at this time," a department representative said.
The State Department warns against travel to Niger due to the threat from terrorist groups in the region.
"Terrorist groups have called for and executed attacks against countries that supported the intervention against terrorist groups in northern Mali, including Niger," its advisory says.
is active in the country, and there is also a threat from al Qaeda, it says.
"The terrorist organization Al Qaeda in the Islamic Maghreb (AQIM) has kidnapped Europeans in the region and continues to threaten to kidnap Westerners, including US citizens, in Niger," the State Department warns.