The US built a base in the desert city of Agadez at the cost of $100m for manned and unmanned surveillance flights.
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Drug seizures, mainly of cocaine and cannabis resin, have soared in the region, according to a UN report.
In March, Niger suspended its military cooperation with the US after leaders severed ties with France last year.
Since the repeal of an anti-migration law last year, migrants and smugglers have flocked back to the city.