The books included a 1937 pamphlet on small arms training and 1970 instructions on how to use standard mortars.
Also confiscated was a Vietnam-era soldiers' handbook and a guide on how to use grenades and "pyrotechnics".
Mr Maddox does not record whom he purchases books from, so it might be difficult for the military to trace who sold the titles to the store.
"It was polite, but it was still intimidating," Mr Maddox said of the raid.
"All the current bookstore owners will be looking at their shelves now."
Mr Maddox says the military police acknowledged they had been tipped off by a serving member of the Defence Force who later asked if he could "photocopy the books".
Australian Booksellers Association chief Joel Becker suggested Defence was being a little too cautious in the age of WikiLeaks, but said: "Sometimes agencies have to respond to complaints."
Questions to Defence about the raid and possible further action went unanswered.