The incident happened in June and the video of the drug bust was released recently.
Special Agent James Spero of U.S. Homeland Security Investigations confirmed the inspections were legal because the vessels were "not flying a country's flag".
Footage shows another boat approach the submersible with crew members on board shouting as they edge closer to it.
Two boats and a jet-ski can be seen chasing down a "narco sub" at pace, as one guardsman yells "Stop your boat now!" in Spanish.
The cutter then launched a helicopter beyond the line of sight of the submersible, and directed the two smaller boats to its location.
Before the sub was able to slip underwater, three commandos from US Coast Guard Cutter Munro (WMSL 755) jumped on the moving vessel.
When asked if the seizures were unusual, Spero said that "homemade" submarine seizures are "not all that unusual", and added that the Coast Guard "sees this amount of drugs every couple of months". Stephen Brickey told ABC News.
The Coast Guard said more than 17,000kg of cocaine and 400kg of marijuana worth a combined estimated $569 million have been seized in 14 separate operations targeting suspected drug smuggling off the coast of Mexico between May and July, 2019. Once they're filled with drugs and deployed, Brickey said they're nearly impossible to detect without prior intelligence or an aircraft.
Driving the cocaine-filled vessel were five suspected drug smugglers.
He said self-propelled semi-submersible vessels are sometimes used by traffickers to smuggle drugs in the open sea.