"...the Minister of Public Security Jose Maria Tijerino stressed that this huge, powerful military force would be under the command of the US Coast Guard and not the US Navy."
They pulled the whole fleet out of the gulf, and put it in Costa Rica under the command of the US Coast Guard, which itself is under command of "Homeland Security". So the newly-created Homeland Security department now controls the gulf fleet, and not the US Navy. i.e., a substantial chunk of the navy is no longer under control of the US Navy.