Fahad Abdulhadi al-Dusari was found guilty of shooting dead Mubarak bin Mohammed al-Dusari following a dispute, the ministry said in statement carried by SPA state news agency.
He was executed in the region of Riyadh, it said.
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Saudi Arabia imposes the death penalty for offences including murder, drug trafficking, armed robbery, rape and apostasy.
Most people executed are beheaded with a sword.
There were no beheadings during the Muslim fasting month of Ramzan, which began in the kingdom on June 6.
However, executions resumed on Sunday when authorities put a Saudi murderer to death.
Human rights group Amnesty International says the kingdom carried out at least 158 death sentences last year, making it the third most prolific executioner after Iran and Pakistan.
Amnesty's figures do not include secretive China.
The London-based watchdog says the Saudi rate of executions this year is "higher than at the same point last year".
Murder and drug trafficking cases account for the majority of Saudi executions, although 47 people were put to death for "terrorism" offences on a single day in January.
They included prominent Shiite cleric Nimr al-Nimr, whose execution prompted Iranian protesters to torch Saudi diplomatic missions, leading Riyadh to sever relations.
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