The weapons were uncovered as part of a planned search of a house at Chestnut Drive, Cluain Ard, Cobh, where the three men who are in their mid 30s to early 50s were arrested.
Gardai say the investigations that led to the arrests were existing operations, and were not directly linked to the inquiry into the murder of dissident republican Aidan O’Driscoll, who was shot dead in Blackpool, Cork last week and whose funeral was held yesterday.
Mr O’Driscoll, a former member of the Real IRA was shot four times on the Old Commons Road near Blackpool Church on Wednesday, December 7.
The search that led to this week’s arrests took place shortly before 8pm on Wednesday, December 14, and a quantity of ammunition was seized along with the firearms.
It is understood that the weapons in question are a handgun and a sawn-off shotgun.
The scene has been preserved for technical examination.
The three men were detained at Cobh and Midleton Garda Stations under Section 30 of the Offences Against the State Act, 1939, and were still being questioned by gardaí yesterday evening.
The provisions of the act under which the three were arrested allows gardaí to detain the men for up to 72 hours.
Garda have tracked dissident activity in Cork in recent years, following threats of vigilantism against drug dealers in the city.
In 2009, leaflets were distributed across a number of pubs in Cork warning suspected drug dealers that they would be shot if they refused to cease selling drugs in the city.