Friday's flash floods, caused by heavy rain, came two weeks after flash floods near the Dead Sea killed 21 people, a lot of them children.
In all, 12 people were killed, including two children and a diver who had been involved in rescue efforts, according to state media and Jordanian government spokeswoman Jumana Ghuneimat.
Hundreds of tourists visiting Jordan's ancient city of Petra have been moved to higher ground after the flash floods in several locations.
At least nine people, including a young girl, were killed as flash floods engulfed multiple cities in Jordan on Friday, a government official said. Rescuers continued the search for missing people around the Wala reservoir in central Jordan on Saturday.
Among those confirmed dead after torrential rains swept the south of the kingdom were six people found in the Madaba area southwest of the capital Amman.
Jordanian army troops deployed helicopters and armoured vehicles to help search for the missing and assist residents threatened by the floods, state television reported.
Amateur video posted online showed a powerful torrent rushing through the steep, narrow canyon through which visitors reach the Treasury, the main attraction of Petra, an ancient trading hub carved from rose-colored rock.
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Downpours also triggered a state of emergency in the port city of Aqaba.
To the east, three people were killed near Dabaa on the Desert Highway, one of Jordan's three main north-south arteries, while one was killed near Maan in the south.
In Wadi Musa, the town next to Petra in southern Jordan, water surged from nearby mountains into a dry riverbed running through the community.
Ghneimat urged residents of the stricken areas and low-lying regions to evacuate their homes, saying that heavy rains were expected to continue to lash Jordan Friday night and Saturday.
The government spokeswoman said 3,762 tourists were evacuated. The tourism and education ministers resigned over the Dead Sea flooding.
The education ministry ordered schools closed nationwide on Saturday amid warnings of more heavy rains.