Abulrahman al-Qarni shot dead fellow Saudi Mushabab al-Khathami during a dispute, said the ministry statement carried by state news agency SPA.
The man was beheaded in the town of Al-Baha in southwestern Saudi Arabia, SPA reported.
The beheading brings to six the number of executions carried out in Saudi Arabia so far in 2012, according to an AFP tally based on official reports.
The United Nations High Commissioner for Human Rights voiced alarm last month at the almost threefold increase in executions in Saudi Arabia last year.
Amnesty International said the kingdom executed 79 people in 2011.
Saudi Arabia applies the death penalty for a wide range of offences, including rape, murder, apostasy, armed robbery and drug trafficking.
In 2010, 27 people were executed, according to the UN, citing a report by Human Rights Watch.
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