New York-based watchdog Human Rights Watch (HRW) slammed the punishment as "outrageous."
The ministry later also announced, in statements carried by the official SPA news agency, that a Saudi was beheaded in the southwestern region of Assir for the murder of a fellow citizen.
The five were executed in the town of Jizan, also southwest Saudi Arabia.
The beheadings today bring the number of people executed in the kingdom this year to 47, according to an AFP tally.
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Their bodies were removed from the area a few hours later, according to witnesses.
In a picture on microblogging website Twitter, five men are seen hanging from a rope tied to their waists on a horizontal bar between two cranes, in a public display which Saudi authorities refer to as "crucifixion."
The ministry said that Khaled, Adel and Qassem Saraa, three brothers, as well as Saif Ali al-Sahari and Khaled Showie al-Sahari had formed a gang which committed "several crimes in various regions in the kingdom and robbed stores."
In remarks emailed to AFP, HRW's Middle East researcher Adam Coogle said "Saudi authorities have once again made headlines for beheading five men and displaying their decapitated bodies in public."
"Regardless of the accusations against them, this outrageous punishment serves as a gruesome reminder of the deficiencies of Saudi Arabia's criminal justice system," he said.
"If Saudi Arabia is serious about reform, as it has claimed, it should create a penal code, uphold fair trial rights, and cease using inhuman punishments."
In March, a Saudi firing squad executed in public seven men convicted of armed robbery despite last-minute appeals by rights groups at the time that their lives be spared.
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under Saudi Arabia's strict version of sharia, or Islamic law.