"Intelligence confirmed that the vessel was involved in illicit narcotics smuggling, transiting along a known narco-trafficking route, and carrying narcotics," the US Southern Command announced in a post on social media.
The announcement said the boat was in international waters when it was struck by Joint Task Force Southern Spear.
The latest operation was the 21st known attack on drug boats by the US military since early September in what it has called a justified effort to disrupt the flow of narcotics into the United States.
The strikes have killed more than 80 people, according to Pentagon figures. Lawmakers in the US Congress, human rights groups and US allies have raised questions about the legality of the attacks.
The Trump administration has said it has the legal authority to carry out the strikes, with the Justice Department providing a legal opinion that justifies them and argues that US military personnel who carry out the operations are immune from prosecution.
Also on Sunday, Secretary of State Marco Rubio said the State Department would designate an alleged drug organisation, Cartel de los Soles, as a "foreign terrorist organization", which makes it a crime for anyone in the United States to provide material support to the group.
US officials have accused Cartel de los Soles of working with the criminal organisation Tren de Aragua to send narcotics to the United States.
The Trump administration has said Venezuelan President Nicolás Maduro leads Cartel de Los Soles, which he denies.
The Pentagon has deployed warships, fighter jets and a nuclear submarine to the Caribbean as US officials consider taking military action against the Maduro government.
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