The operation was uncovered at a site describing itself as a gearbox repair business on an industrial estate in Hailsham, East Sussex.
Police arrested three men found leaving the building and had to use a Taser on one of them, a National Crime Agency spokesperson said.
Two hand guns and some ammunition were found at the site, which has been cordoned off while investigations continue.
Greg Akehurst, 29, of no fixed address, and Mark Kinman, 63, of Bramwell Mews, Hailsham, were both charged with possessing a firearm on Wednesday.
Kyle Wood, 30, of Gratwicke Drive, Littlehampton, was charged with the same offence as well as possessing ammunition.