The Pentagon delegation, headed by Christopher Maier, assistant secretary of defence for special operations, was received by Nigerien defence minister General Salifou Modi, said a ministry communique.
About 650 American troops, and several hundred contract workers, are in the central African state as part of regional efforts to suppress jihadist groups.
The military government has increasingly turned to Russia for security backing.
Niger said it aims for an "orderly" and "safe withdrawal as soon as possible" of American soldiers, whose presence the regime has declared to be "illegal".
Niger's military leaders, who came to power in coup last July, have already expelled French troops that have traditionally provided security in the former colony.
Niamey said it was the first official meeting since Niger in March pulled out of a military cooperation agreement with the United States.
Washington accepted in April to withdraw its forces, most of whom are on a drone base near Agadez in the north that cost a reported $100 million to build.
On Tuesday, Prime Minister Ali Mahaman Lamine Zeine said Niger severed its military cooperation due to "threats" made by US officials.
According to Zeine, Washington threatened to impose sanctions if Niger signed an agreement to sell uranium to Iran, though he insisted no such deal had been signed.
The United States has a development aid accord with Niger worth about $500 million over three years, according to the foreign ministry, which said it would continue.
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