The nine youths were confirmed dead by rescue authorities, according to Israeli media reports Thursday.
Eight of the deceased were female and one was male.
About 25 teens registered for a pre-army preparatory course in Tel Aviv were hiking in Nahal Tzafit on Thursday afternoon when the flooding began. Some 15 were rescued mostly unharmed.
Apache helicopters were searching the area and divers had prepared to go into the stream to find missing hikers.
The Ministry of Education had warned schools not to hike in the area, according to Channel 10 news.
“The trip was not reported to us, our situation room was not told in advance and we did not give any permission for such a trip,” the ministry said in a statement.
The trip was not under the auspices of the Education Ministry or the Defense Ministry, The Times of Israel reported.
The hikers were all 17- and 18-year-olds on a bonding trip ahead of entering the pre-military academy in September.
Police spokeswoman Meirav Lapidot told reporters before the announcement of the dead teens, “We will keep going until we find them all. We are preparing for a long night of search-and-rescue operations.”
Heavy rain fell in southern Israel on Wednesday and Thursday, and throughout the country, which is unusual for this time of year.
Two teens, a Bedouin and a Palestinian, died in flash floods on Wednesday, according to reports.