The three convicts had attempted to "smuggle a large amount of hashish by sea" into Saudi Arabia, the ministry said in a statement published on the official SPA news agency.
They were executed in the eastern port city of Dammam, it said.
Saudi executions are usually carried out by beheading with a sword.
According to AFP tallies, their cases bring to 145 the number of locals and foreigners executed in the conservative Islamic kingdom this year, compared with 87 in 2014.
London-based Amnesty International says Saudi Arabia had the world's third-highest number of executions last year, far behind China and Iran, but ahead of Iraq and the United States.
Under the kingdom's strict Islamic legal code, murder, drug trafficking, armed robbery, rape and apostasy are all punishable by death.