The Yemenis were convicted of forming a gang that killed two men and a woman in three separate attacks on homes in the southern province of Assir, it said in a statement cited by the SPA news agency.
In each attack, they also stole cash and other items, the statement added.
They were executed at Abha in the southwest of the Gulf kingdom.
The seventh convict, a Saudi, was executed in the northern city of Tabuk after being convicted of smuggling pills, the ministry said.
The kingdom is governed under a strict form of Islamic law, with suspects convicted of "terrorism", murder, rape, armed robbery and drug trafficking facing the death penalty.
Today's executions take the total number of judicial killings in the ultra-conservative country so far this year to 130, according to data compiled by AFP.