The cyclone struck mainland Oman and Yemen early Saturday, dumping almost three years' worth of rain on Salalah in 24 hours.
Three wounded Asians were rescued and civil defence teams said they had saved hundreds of people including 260 foreign sailors trapped at sea.
State-run Oman Television showed footage of large areas covered with floods in Dhofar and the nearby Al-Wusta provinces. More than two dozen people are still missing.
The NCM also predicts that Mekunu will intensify into a Category 2 cyclone over the next 12 hours, with an expected wind speed of between 155 to 165 km/h. The strength of the storm over Oman has now been downgraded from category three to category one. The girl died after she was swept against the walls by the wind whereas the other got washed away in a auto.
The Saudi meteorological authority said on Twitter Sunday that winds blew at 60 kilometers (over 35 miles) per hour, kicking up blinding dust storms. The city's port remains closed. Capt. Tarek al-Shanfari of the Royal Oman Police's public relations department said there had been at least three fatalities in the storm, including the death of a 12-year-old girl who was hit in the head by a door flung open by the wind.
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Rip currents will also be a concern at affected beaches over the busy holiday weekend, especially along the northern Gulf Coast. That system on Sunday and Monday likely will continue moving north and dumping heavy rains along the Gulf Coast .
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India's Ministry of External Affairs said embassy officials had arranged for food for 460 people (145 Indians and 315 Bangladeshi nationals) at a camp in Taqah.
Kafin said that 1,000 families were evacuated to safety after there homes were affected by flooding. The island of Socotra has been declared a disaster zone by the government.
Debris and sea foam litters a beach after Cyclone Mekunu in Salalah, Oman, Saturday, May 26, 2018.
Yemeni officials also reported damage in the east of the country along the border with Oman, reports AP.