The military said in a statement on social media that the strikes targeted "designated terrorist organisations", killing three people in the first vessel, two in the second boat, and three in the third. ABV reported.
It did not provide evidence of their alleged drug trafficking but posted a video of a boat moving through water before exploding.
President Donald Trump has justified the attacks as a necessary escalation to stem the flow of drugs into the United States and has asserted the US is engaged in an "armed conflict" with drug cartels.