Government spokeswoman Jumana Ghneimat said authorities had found alive four Israeli tourists who had gone missing in the Wadi Rum desert in southern Jordan but were looking for two more.
Two women and a girl died in severe floods in Dabaa, and another girl died in Madaba. Rescuers continued the search for missing people around the Wala reservoir in central Jordan on Saturday.
Hundreds of tourists visiting Jordan's ancient city of Petra have been moved to higher ground after the flash floods in several locations.
Elsewhere, rising water levels forced the closure of a desert highway.
Divers have been searching for five people whose vehicle was swept away by floods in the Madaba area, southwest of the capital Amman.
Israel Defense Forces (IDF) said that its search and rescue team deployed with an Israel Air Force (IAF) helicopter was able to locate and rescue the civilians.
A civil defence source told AFP that another child died in the Madaba area, also south of Amman, when the auto the child was in was submerged in water.
The torrents came two weeks after 21 people, majority children, were killed in flash floods near the Dead Sea.
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Authorities declared a state of emergency in the Red Sea port city of Aqaba further south as downpours started in the afternoon.
In Petra, flood waters in some areas rose up to 4m (13ft), state TV reported.
It broadcast footage showing people standing on both sides of the main road in Petra and along the desert highway trying to stay clear of the floods.
Cadres of the Petra Directorate managed to secure 3,500 tourists from the "unprecedented" flash floods that raided Wadi Musa, on November 9, 2018, according to Petra District Director, Sultan Al Madi.
Ghneimat urged residents of the stricken areas and in low-lying regions to evacuate their homes, saying that heavy rains were expected to continue to lash Jordan Friday night and Saturday.
Severe floods on Friday hit Maan governorate, Wadi Mousa area, Petra, Madaba and other areas in Jordan following heavy rainfall across the Kingdom.
Friday's floods came two weeks after 21 people, including middle school students, were killed in flash floods near the Dead Sea.