Heavy rains and high winds since Monday have caused rivers to flood near two key north-south highways, while several roads are blocked near the Red Sea resort of Eilat.
The emergency services said they had stepped up operations to rescue holidaymakers caught by floods during a peak travel period, as the Muslim holy month of Ramadan coincides with Jewish Passover and Christian Easter.
"The army and the emergency services recently located the bodies of the two people missing in the flood," the army said in a statement Tuesday.
The bodies of a man and a woman were found in the Aravah region of the Negev desert, police said, after earlier reporting that two people were missing near the area's highway.
Some 60 people have been rescued so far, including some who police said had been "swept away in their vehicles".
Police said Tuesday afternoon they were expecting more floods across the country.
Another woman earlier reported missing was found to be safe.
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