The death toll from flash floods unleashed by heavy rains in Jordan has risen to 12, according to local media, and forced authorities to evacuate more then 4,000 tourists from the ancient city of Petra.

Saturday’s reports came a day after floods struck in several areas of Jordan, including Petra, and the searches for missing people continue.

Government spokeswoman Jumana Ghneimat and civil defence officials say the death toll rose early on Saturday, after another body was found in the Madaba region south of the capital of Amman. Six people are known to have died there.

Hundreds of Petra visitors ran for higher ground on Friday as water surged through a narrow canyon leading to the Treasury, Petra’s main attraction.

The visitors were taken to safe areas before flash floods inundated parts of the mountainous city famed for its carved rock ruins, government spokeswoman Ghneimat said.

Flash floods at Petra forced 4,000 tourists to flee. Photograph: -/AFP/Getty Images

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.

“Our embassy in Tel Aviv contacted the Israeli foreign ministry for information on the identities of the missing Israelis,” Ghneimat said in statements carried by the state news agency Petra.

Authorities declared a state of emergency in the Red Sea port city of Aqaba further south as downpours started in the afternoon.

Members of Jordan Civil Defence rescue team search for a missing girl in Madaba. Photograph: Andre Pain/EPA

A major highway that links Amman with the south was also closed. The government announced the closure of universities and schools on Saturday and mosques were opened to shelter civilians in areas hit by the floods.

Two weeks ago, 21 people, mainly children, died after they were swept away in flash floods on a school outing in the Dead Sea region, in one of the country’s worst natural disasters in decades.

Politicians and members of the public criticised the emergency services at the time, saying crews had been unprepared, and two ministers were forced to resign after a parliamentary committee found negligence.