The ministry said three assailants also died in an exchange of fire.
In Yemen, a security source said earlier that suspected Al-Qaeda gunmen attacked a military post on the Saudi border, triggering a clash that killed one soldier and wounded another.
The assailants used machineguns and rocket-propelled grenades to attack the Yemeni side of Wadia border post, the source said, adding that the gunmen managed to flee.
The crossing is in Yemen's southeastern province of Hadramawt, whose rugged terrain provides hideouts for militants of Al-Qaeda in the Arabian Peninsula.
Local Yemeni officials told AFP that today's attack bore "the thumbprints of Al-Qaeda" without elaborating.
Smugglers also do a brisk business across the long and porous border between oil-rich Saudi Arabia and impoverished Yemen.