Search teams were scouring valleys near the historic hill town of Madaba for a young girl who was still missing after Friday's floods, civil defence spokesman Iyad Amru told state television.
Five people have already been confirmed dead in the area southwest of the capital Amman after torrential rains swept the south of the kingdom.
Amru said two girls had gone missing in the Madaba region, later announcing that one of their bodies had been found.
He added that the floods in Petra are within their natural conditions and that the cadres of the Petra Commission are now working on counting tourists and evacuating them to their hotels, adding that the areas that have been exposed to the floods are: Wadi Musa and other areas, adding that the Desert Highway is open, under normal traffic conditions and with no reported accidents so far.
In Petra, the ancient trade hub carved into rose-hued rocks, heavy rains began at around 1 p.m. Friday and last for about 40 minutes, said Rafael Dorado, 41, a tourist from Spain.
It broadcast footage of tourists sheltering on high ground on both sides of the access road to Jordan's biggest attraction.
Jordan's state news agency Petra quoted government spokeswoman Jumana Ghunaimat as saying that evacuations will be carried out in coordination with the local councils of municipalities and provinces, directors of public works and public security, and the civil defense.
Authorities evacuated 3,762 tourists from the ancient city of Petra, an archeological site and key tourist destination in southern Jordan, amid the bad weather, Ghneimat said. Trips to tourists sites have also been suspended.
The latest deaths come after Oct 25 flash floods in the Dead Sea region of the kingdom killed 21 people, a lot of them children on a school trip.
She said more heavy rain was expected on Saturday and residents in affected areas were being urged to evacuate their homes.
Last week, Jordan's education and tourism ministers resigned after the deaths of 21 people, mostly schoolchildren on an outing, who were swept away in flash floods near the Dead Sea in late October, state media said.