The Pentagon is working with Niger officials to find a way for US troops to stay in the country – a key base for counterterrorism operations in sub-Saharan Africa – following a weekend directive that they leave.

Last week a high level-delegation of US officials, including Assistant Secretary of State for African Affairs Molly Phee, Assistant Secretary of Defence for International Security Affairs Celeste Wallander and the head of US Africa Command Gen Michael Langley, travelled to Niger to meet with members of the military junta.

Pentagon deputy press secretary Sabrina Singh said on Monday the US officials had “lengthy and direct” discussions with the junta officials that were also in part spurred by concerns over Niger’s potential relationships with Russia and Iran.

“We were troubled on the path that Niger is on,” Singh said.

On Saturday, following the meeting, the junta’s spokesperson, Col-Maj Amadou Abdramane, said US flights over Niger’s territory in recent weeks were illegal. Meanwhile, Insa Garba Saidou, a local activist who assists Niger’s military rulers with their communications, criticised US efforts to force the junta to pick between strategic partners.

“The American bases and civilian personnel cannot stay on Nigerien soil any longer,” he told The Associated Press.

Singh said the US was aware of the March 16 statement “announcing the end of the status of forces agreement between Niger and the United States. We are working through diplomatic channels to seek clarification. These are ongoing discussions and we don’t have more to share at this time.”

The junta has largely been in control in Niger since July when mutinous soldiers ousted the country’s democratically elected president and months later asked French forces to leave.

The US military still had some 650 troops working in Niger in December, largely consolidated at a base farther away from Niamey, Niger’s capital. Singh said the total number of personnel still in country, including civilians and contractors, is roughly 1,000.

The Niger base is critical for US counterterrorism operations in the Sahel and has been used for both manned and unmanned surveillance operations, although Singh said the only drone flights being currently conducted are for force protection.

In the Sahel the US has also supported local ground troops, including accompanying them on missions. However, such accompanied missions have been scaled back since US troops were killed in a joint operation in Niger in 2017.

• An AP report