The "hard landing" of the unarmed MQ-9 Reaper aircraft damaged the runway at Diori Hamani International airport in the Niger capital Niamey, but no injuries were reported, according to a statement from the US Air Forces in Europe and Africa public affairs directorate.
"The US government is working closely with the government of Niger to secure the scene and mitigate inconveniences caused by the incident," the statement sent to AFP added.
"The cause of the incident is currently under investigation."
"The aircraft nosed down" around 03:40 am (0240 GMT), a Nigerien airport source told AFP, adding that the drone was originally thought to be French.
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The airport stayed closed until 12:30 pm to repair the damage to the runway, the source said.
A plane carrying pilgrims on their way back from Mecca had to be diverted to Ouagadougou, airport authorities in Burkina Faso said.
Planes could be seen landing at Niamey airport again in the afternoon, a security source said.
Last month, the US military announced it would shift its drone flights from Niamey to a base about 500 miles (800 kilometres) further north in Niger, allowing Washington to better track Islamist fighters in the region.
The northern location will give the unmanned, robotic aircraft easier access to a desert route linking southern Libya and northern Mali, which is used to move arms and Islamist fighters.
The French military also flies drones out of Niamey.