The men -- two Saudis and a Bahraini -- were killed in an exchange of gunfire with police in the city of Saihat in the district of Qatif on July 14, the ministry said.
Police seized three machine guns, a pistol, ammunition and more than 10 kilos of explosives, official news agency SPA reported a ministry spokesman as saying.
He said the men were wanted for their involvement in deadly attacks against the police, as well as an attack on a vehicle used to transport cash, abductions and weapons trafficking.
Most of Saudi Arabia's Shiites live in the oil-rich east, where they have long complained of marginalisation.
The area has been rocked by unrest since 2011, when Shiite protests erupted to demand equality in the Gulf kingdom.
Authorities have blamed the violence on "terrorists" and drug traffickers.
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