The monks were arrested in the city of Siem Reap and belonged to Pur Langka pagoda, the Cambodia Daily reported.
Among the two monks, one was a senior at the pagoda.
Pich David, 36, "had been under suspicion for some time as he always argued with the chief monk and did not follow Buddhist doctrines", a police official said.
"When we entered the room we found alcohol, some condoms and a pipe for smoking 'ice' (crystal methamphetamine}," the official said.
On Sunday, the court charged the two monks with drug use.
Pur Lanka pagoda's chief monk Keo Khouy said this was the second time the elder monk has been thrown out of the pagoda.
"Pich David was expelled in 2012 for bad behaviour but we allowed him to return in 2013 after he pleaded with the pagoda authorities to come back and promised to adhere to the Buddhist doctrine and to follow the rules of the pagoda," he said.
Earlier this month, the chief monk at a pagoda in Kompong Speu province was defrocked after being caught drinking with police officers at a karaoke parlour in Kandal province.
Under Buddhist doctrine, monks must refrain from alcohol, drugs and sex.