Prior to the operation, the troops had been given a directive from US Defense Secretary Pete Hegseth to kill everyone on board, the Washington Post and CNN both reported, citing unnamed sources familiar with the operation.
"The order was to kill everybody," one of the sources told the Post.
The alleged incident occurred on September 2 during the first publicized strike in a series of attacks against boats in both the Caribbean and eastern Pacific that Washington claims were trafficking drugs in international waters.
President Donald Trump's administration has not offered evidence to back up the allegations behind its campaign, which has killed at least 83 people, according to an AFP tally of publicly released figures.
On September 2, the US military saw two survivors of an initial strike clinging to the burning vessel, then proceeded to strike them again, the Washington Post reported.
After the September 2 strike, protocols were changed to rescue any survivors, the Post added.
According to CNN, it was not clear whether Hegseth knew there were survivors before the second strike was carried out.
The Intercept initially reported on the follow-up attack on September 10.
On Friday, Hegseth posted on social media that "current operations in the Caribbean are lawful under both US and international law", responding to what he called "fake news," though he did not specifically mention the September operation.
The US Justice Department has defended the strikes as consistent with the law of armed conflict and the government has signaled it will continue the operations.
Responding to the Washington Post report on Friday, Democratic congressman Seth Moulton said on X that the "killing of survivors is blatantly illegal."
"Mark my words: It may take some time, but Americans will be prosecuted for this, either as a war crime or outright murder," said the Marine veteran.
The Pentagon has told Congress the United States is in "armed conflict" with Latin American drug cartels, designating them as terrorist groups and describing suspected smugglers as "unlawful combatants."
The report comes in the midst of political furor over a video released by Democratic members of Congress this month, addressing the military and saying troops have the right to refuse illegal orders.
Though they did not specify which orders they were referring to, Trump has labeled the group of lawmakers "traitors."
UN Human Rights chief Volker Turk has urged Washington to investigate the strikes' legality, saying there was "strong evidence" they constitute "extrajudicial" killings.
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