Search teams were scouring valleys near the historic hill town of Madaba for two young girls still missing after Friday's floods, civil defence spokesman Iyad Amru told state television in an update.
At least 11 people were killed and dozens were injured on Friday after floods ripped several areas of the Kingdom, the government said Friday. The Jordanian military said that that it has sent soldiers and helicopters to assist in search operations.
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.
Jordan has seen a series of deadly floods in recent weeks, including one in late October that swept away a school bus near the Dead Sea, killing 21 people, mostly schoolchildren.
Politicians and members of the public criticised the emergency services for being unprepared and two ministers were forced to resign due to negligence.
The Madaba region, the Maan governorate and the ancient city of Petra were among the areas hit hardest by Friday's storms.
Heavy downpours triggered the flash floods, forcing more than 3,500 worldwide and domestic tourists to be evacuated from the tourist city of Petra in southern Jordan, according to Jumana Ghuneimat, Jordan's minister of state for media affairs and government spokeswoman.
The visitors were taken to safe areas before flash floods inundated parts of the mountainous city famed for its carved rock ruins, government spokesperson Jumana Ghunaimat said.
Dozens were evacuated from the area.
In an earlier statement, Ghunaimat said two women and a girl were killed in Madaba province when their vehicle was swept away, adding that nine people were admitted to hospital, including some in critical condition.
Authorities declared a state of emergency in the Red Sea port city of Aqaba further south as downpours started in the afternoon.
More rain is expected on Friday night and Saturday, and schools have been opened to evacuees and those affected by the floods.
In Petra, flood waters in some areas rose up to 4m (13ft), state TV reported.