The statement by US Southern Command, which oversees South America, did not reveal where the attacks occurred.
Previous attacks have been in the Caribbean Sea and in the eastern Pacific Ocean.
A video posted by Southern Command on social media shows the boats travelling in a close formation, which is unusual, and the military said they were in a convoy along known narco-trafficking routes and "had transferred narcotics between the three vessels prior to the strikes".
The military did not provide evidence to back up the claim.
The military said three people were killed when the first boat was struck, while people in the other two boats jumped overboard and distanced themselves from the vessels before they were attacked.
Southern Command said it immediately notified the US Coast Guard to activate search and rescue efforts.
The attacks occurred on Tuesday local time. Southern Command's statement did not say whether those who jumped off the boats were rescued.
Calling in the Coast Guard is notable because the US military drew heavy scrutiny after American forces killed the survivors of an attack in early September with a follow-up strike to their disabled boat.
Some Democratic lawmakers and legal experts said the military committed a crime, while the Trump administration and some Republican lawmakers say the follow-up strike was legal.
The latest attacks bring the total number of known boat strikes to 33 and the number of people killed to at least 110 since early September, according to numbers announced by the Trump administration.
President Donald Trump has justified the attacks as a necessary escalation to stem the flow of drugs into the United States and asserted the US is engaged in an "armed conflict" with drug cartels.
Along with the strikes, the Trump administration has built up military forces in the region as part of an escalating pressure campaign on Venezuelan President Nicolas Maduro, who has been charged with narco-terrorism in the United States.
Meanwhile, the CIA was behind a drone strike last week at a docking area believed to have been used by Venezuelan drug cartels, according to two people familiar with details of the operation who requested anonymity to discuss the classified matter.
It was the first known direct operation on Venezuelan soil since the US began strikes in September, a significant escalation in the administration's pressure campaign on Maduro's government.
With Reuters
23°C