It was the latest action by the US against boats and vessels in Latin America that it said were involved in drug trafficking.
The joint task force intercepted a floating refuelling station that supported illicit drug trafficking operations at sea in the Eastern Pacific, the Southern Command said in a statement.
It added that the people on board the vessel were removed and will be transferred to Ecuadorian authorities.
A video accompanying the announcement showed military personnel boarding a ship, followed by a helicopter flying overhead and finally a projectile striking and sinking it.
The statement also indicated that US forces continue to conduct "precise and professional operations to dismantle the logistical networks that fuel drug trafficking in the Western Hemisphere".
Ecuadorian authorities did not immediately comment.
The sunken vessel, whose name has not been released, was the fifth targeted by US forces in less than two weeks.
The fishing vessel María Candelaria was struck last week in the Pacific, according to information from US Southern Command, in co-ordination with Ecuadorian authorities.
The Ecuadorian navy located 26 crew members from that vessel, who arrived on Sunday in the port city of Manta. Eight fishermen from the Conquista II were also located, while their families on the mainland demanded information about their whereabouts.
The other two vessels were the OM2 and Los Tres Hermanos, whose crew members say they were sunk. Southern Command recently identified them as "floating refuelling stations for multiple vessels engaged in illicit drug trafficking operations," in posts on X.
The United States has said all of the boats were linked to Los Choneros, which the US considers a foreign terrorist organisation.
At least 227 people have been killed in 68 US government strikes that began against boats in the Caribbean and Pacific more than a year ago. Critics have questioned the overall legality of the boat strikes as well as their effectiveness.
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