The men were "seriously wounded by the explosion of a mine while they were conducting a search operation at Mount Chaambi targeting terrorist elements on the run," the ministry said, referring to Islamist militants.
It said one of the victims lost a leg and that the other was seriously wounded in the eyes.
It did not say whether the mine was laid by those being pursued in the operation, or if it was a part of the security infrastructure along Tunisia's long and porous western border with Algeria, where arms trafficking is common.
"According to preliminary reports, the mines were laid by the (fugitive) group," which is thought to be hiding in the mountainous region, the security official said.
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A gunfight that took place earlier in the day had complicated the evacuation of the two guards who were finally taken to hospital in the region capital Kasserine where they were operated on, medical and security sources said.
Shortly afterwards, the authorities claimed to have broken up an al-Qaeda recruitment cell and arrested 16 suspected members.
Since the revolution in January 2011 that ousted veteran strongman Zine El Abidine Ben Ali, Tunisia has witnessed a wave of sometimes deadly unrest blamed by the authorities on hardline Islamists, who were repressed under the former president.
Algeria, Libya and Tunisia agreed in January to strengthen cooperation to secure their common borders, combat arms trafficking and crack down on organised crime.