A US-designated terrorist organisation operated the vessel, Hegseth said on social media, but did not name which group was targeted.
He said three people were killed in the strike.
It's at least the 15th such strike carried out by the US military in the Caribbean or eastern Pacific since early September.
"This vessel—like EVERY OTHER—was known by our intelligence to be involved in illicit narcotics smuggling, was transiting along a known narco-trafficking route, and carrying narcotics," Hegseth said in a posting on X.
The US military has now killed at least 64 people in the strikes.
Trump has justified the attacks as a necessary escalation to stem the flow of drugs into the US.
He has asserted the US is engaged in an "armed conflict" with drug cartels, relying on the same legal authority used by the Bush administration when it declared a war on terrorism after the September 11, 2001, attacks.
The White House has repeatedly rebuffed US lawmakers' demand the administration release more information about the legal justification for the strikes, as well as greater details about which cartels have been targeted and the individuals killed.
"Narco-terrorists are bringing drugs to our shores to poison Americans at home", Hegseth said in his post about the latest strike, and the defence department "will treat them EXACTLY how we treated Al-Qaeda".
Senate Democrats renewed their request for more information about the strikes in a letter on Friday to Secretary of State Marco Rubio, Director of National Intelligence Tulsi Gabbard and Hegseth.
"We also request that you provide all legal opinions related to these strikes and a list of the groups or other entities the president has deemed targetable," the senators wrote.
Among those signing the letter were Senate Minority Leader Chuck Schumer and senators Jack Reed, Jeanne Shaheen, Mark Warner, Chris Coons, Patty Murray and Brian Schatz.
The letter says thus far, the administration "has selectively shared what has at times been contradictory information" with some members, "while excluding others".
Earlier on Friday, the Republican chairman and ranking Democrat on the Senate Armed Services Committee released a pair of letters sent to Hegseth, written in late September and early October, requesting the department's legal rationale for the strikes and the list of drug cartels the Trump administration has designated as terrorist organisations in its justification for the use of military force.
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