The military said on Thursday night that it had recovered "10 survivors" and retrieved the remnants of the boat.
According to a statement from the armed forces' public relations office, the "patrol boat capsized at the mouth of the Senegal River (north) this morning around 9 am. Three sailors are missing".
The vessel "was on a liaison mission and is believed to have encountered heavy swells following a deterioration in weather conditions," it added.
The military has deployed "air, maritime and land assets" to locate the three missing.
The 1,640-kilometre (1,020-mile) Senegal River forms the country's natural border with Mauritania and drains into the Atlantic near the city of Saint-Louis.
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