The video, featuring Pete Hegseth, showcased Donald Trump's executive order to "unleash American drone dominance."
A representative for Metallica confirmed the song's unauthorised use, leading to the Pentagon re-uploading the video without the music.
Metallica has a history of enforcing copyright, notably against Napster, and has previously distanced their music from military use.
This incident follows a trend of numerous musicians, including The White Stripes, Elton John, Taylor Swift, and Beyoncé, objecting to their music being used by Donald Trump's campaigns without permission.