Benin and Niger have engaged in increasing tit-for-tat accusations in recent weeks over the movement of goods, despite West African bloc ECOWAS in February lifting sanctions imposed on Niger's military rulers.
Relations over the border are also complicated by a spillover from expanding jihadist conflicts in Niger and Burkina Faso that increasingly threaten Benin and its Gulf of Guinea neighbors Ghana and Togo.
Benin initially announced the opening of its border at the same time as the lifting of ECOWAS sanctions.
But the border has remained closed on the Niger side, irritating Beninese President Patrice Talon, who said Niger was treating them like "an enemy."
Benin had until now turned a blind eye to the informal transit to Niger of foodstuffs, particularly cereals, by boat across the Niger River as a way to show solidarity with its neighbor.
A source close to the Benin government confirmed the river crossing had now been closed.
"The river is part of the border. Niger says its borders with Benin are closed. It's a consequence," the source told AFP.
"With the flow of people on the river and the boats whose loading no one controls, if a tragedy occurs it won't be good."
According to a Benin military official in Malanville, a police officer working in the area and local residents who spoke to AFP, the Malanville bridge which provides the border crossing between the two countries remains closed on the Niger side, but the transport of goods across the Niger River is also now prohibited.
"The suspension was gradual. We first banned the passage of goods, now there is no more traffic on the water," a military official told AFP on condition of anonymity as he was not authorised to speak to the media.
"We have been deployed to prevent any boarding here."
A local Malanville resident who only gave a first name Alassane said there was now a large deployment of Benin police and troops in the area.
Several Malanville residents told AFP that Nigeriens were dispersed by troops on the other side as they could not cross the river.
The closure of the river traffic is the latest in a series of decisions impacting trade between the two countries.
Talon blamed informal border trafficking for the increase in the cost of living in Benin, which last month triggered a protest over high costs.
Earlier this month, Benin said it will still allow exports of Nigerien oil through its port of Seme, in the resolution of one of their points of dispute.
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