Surasak Suksri, 37, was arrested in Ratchaburi, while his elder brother Pracha, 48 was arrested in Songkhla.
The pair are accused of using the M16 in an attempt to kill officials, possessing guns and bullets without permission and carrying guns in public places.
They deny the allegations.
Police will interrogate them to try to find more people suspected of complicity in the attack, which occurred in August last year.
Police believed strict searches for drugs and mobile phones smuggled into the jail by Taweesak Nuankaeo, 47, the security guard later wounded, led to police raids that may have motivated affected people to attack him.