Presidential guards were holding Niger President Mohamed Bazoum inside his palace in the capital Niamey, but the presidency said the guards had started an "anti-republican" movement in vain and that Bazoum was well.
West Africa's main regional and economic bloc ECOWAS said it was concerned about an attempted coup and called on the plotters to free Bazoum.
The African Union called on the "treasonous" soldiers involved to stop immediately.
The national army was ready to attack the guards if they did not come to their senses, the presidency said in a statement.
The statement followed reports that presidential guards had cut access to the palace and blocked Bazoum inside, raising concern West Africa's sixth coup since 2020 could be underway.
"The President of the Republic and his family are well," the presidency said on its social media pages without providing further details.
The statement was later deleted amid doubts about who was in control. Soldiers had taken control of all roads leading to the national television station which was playing a movie.
The rest of Niamey appeared calm, with normal traffic on the road and full internet access, a Reuters reporter said.
A military takeover in Niger could further complicate Western efforts to help countries in the Sahel region fight an insurgency that has spread from Mali over the past decade.
Niger has become a pivotal ally for Western powers seeking to help fight the insurgency but facing growing acrimony from the new juntas in charge in Mali and Burkina Faso. It is also a key EU ally in the fight against irregular migration from sub-Saharan Africa.
"The EU condemns any attempt to destabilize democracy and threaten the stability of Niger," its foreign policy chief Josep Borrell said in a post.
France moved troops to Niger from Mali last year after its relations with interim authorities there soured. It is also withdrawing special forces from Burkina Faso due to similar tensions.
The United States says it has spent around $500 million since 2012 to help Niger boost its security.
Germany announced in April that it would take part in a three-year European military mission aimed at improving the country's military.
"Bazoum has been the West's only hope in the Sahel region. France, the US and the EU have spent much of their resources in the region to bolster Niger and its security forces," said Ulf Laessing, head of the Sahel programme for Germany's Konrad-Adenauer-Stiftung think-tank.
He added that a coup would create an opportunity for Russia and other actors to spread their influence in Niger.
Frustrations over state failures to prevent violent attacks on towns and villages partly spurred two coups in Mali and two in Burkina Faso since 2020.
A junta also snatched power in Guinea in 2021, contributing to instability in a region that had begun to shed its reputation as a "coup belt".
There was a thwarted coup attempt in Niger in March 2021, when a military unit tried to seize the presidential palace days before the recently elected Bazoum was due to be sworn in.
On Wednesday morning, military vehicles barred access to the presidential palace in Niamey. Security sources later confirmed that presidential guards were blocking Bazoum inside the building.
Bazoum's election was the first democratic transition of power in a state that has witnessed four military coups since independence from France in 1960.
Military action and community engagement have spared Niger from the brunt of the insurgency, which has killed thousands and displaced over six million across the Sahel.