The bus had been carrying 37 pupils and seven members of staff to the Zara Maeen hot springs area when it was washed away, officials said.
"The IDF has begun assisting in the rescue of the Jordanian children's bus that was swept away adjacent to the Dead Sea on the Jordanian side as a result of flooding in the southern area earlier today", the IDF stated.
The Civil Defence said they have been able to rescue ten of the students from the bus so far and pointed out that the torrential rains could persist. "The soldiers, led by the commanding officer of Unit 669, are assisting in locating the missing in spite of the adverse weather conditions", the statement said.
A child survivor is seen with relatives in a hospital near the Dead Sea, Jordan.
Heavy rains hit Jordan on Thursday afternoon, causing floods in several areas.
At least 16 people, majority children, were killed in a fierce flood on the Jordanian side of the Dead Sea Thursday. Gen. Farid al-Sharaa, speaking after nightfall as large spotlights illuminated the flooded area.
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The Israeli military sent helicopters to help the Jordanian emergency services.
Mustafa al-Basaiah, the director general of the kingdom's Civil Defense, said that 13 of the dead and 21 of about three dozen injured were middle school students. The Minister of Public Sector Development along with CDD are at the scene to follow up with the rescue efforts and the search of missing persons.
The Dead Sea, the lowest point on the earth, is surrounded by steep valley slopes that frequently witness flash floods and landslides.
Prime Minister Omar Razzaz and senior government and army officials oversaw the rescue operation, and instructed state agencies on Thursday to provide all needed assistance to ensure the safety of the students and those trapped.
As the death toll continued to rise Thursday evening, Jordan's King Abdullah II announced that he canceled a visit to Bahrain, which had been scheduled for Friday.