Rescue efforts were ongoing to find a missing girl from a group of youths taking part in a program to prepare them for military service, according to media reports.
Students in such programs are usually around the age of 18.
A major rescue effort had earlier been launched to find what had initially been reported as several missing.
"Police & Emergency teams working together after flash floods struck the south of Israel near the Dead Sea where students were on a day trip," police spokesman Micky Rosenfeld tweeted.
Military helicopters took part in the search in an area known as the Tzafit Stream, which hikers frequent for its desert scenery.
Another police spokesman, Merav Lapidot, said on Israeli television that "instructions to avoid this type of drama" were not respected.
President Reuven Rivlin said on Twitter that "our thoughts go out to our brothers, our children and our loved ones who are dealing with a dramatic situation."
He also called on the public to "respect police instructions".
Two teenagers, a Bedouin and a Palestinian girl, also died in a series of floods that hit Israel and the Palestinian territories on Wednesday, the first of three forecast days of heavy rain.
