A child drowned in the rising waters on Sunday afternoon while authorities said a man previously reported missing had also drowned.
Oman's National Committee for Emergency Management also said that rescue teams pulled the bodies of two men from their home after it was hit by a landslide in the Rusayl industrial area of Muscat province.
In Iran, state television said rescuers found the body of one of five fishermen who went missing off Pasabandar, a fishing village near the Iran's border with Pakistan.
The storm made landfall on Sunday evening, the state news agency reported. Widespread flooding had already damaged commercial and residential properties.
“Cyclone Shaheen has moved away from Muscat and it is making a landfall in Batnah towns, with high wind speeds causing rough seas. People there are cautioned to stay at home unless it is necessary to go out,” Oman's Civil Aviation Authority said in an update broadcast on Oman TV.
People who are living in houses near the beach were being evacuated to shelters set up by the emergency services, the state broadcaster said.
But not everybody was willing to move out, with some choosing to stay in their residences.
“We are not going anyway. We are staying home. It is bad but we will be OK if we stay on the upper floor. The water will not rise up there,” Khamis Al Anboori, who lives in Khaboora, told The National.
Schools and shopping malls have been turned into shelters with evacuated people taking their mattresses and blankets.
“We get free food and drink here but hopefully we will be back home some time tomorrow,” said Ali Al Bahrani, in Sohar.
Oman declared a two-day national holiday on Sunday and Monday, urging people to stay indoors as waves hitting the coast rose to 12 metres and wind speeds reached 120 kilometres per hour.
Muscat International Airport said inbound and outbound flights were being put on hold.
“We are rescheduling flights, both departures and arrivals, according to the weather forecasts. Most of the scheduled flights have been suspended today because of the strong winds and rains” a spokesman for Oman Airports Management Company told The National.
“We are monitoring the situation and following the weather update from the Civil Aviation Authority to decide on the flight movements.”
Hospitals are receiving many injured people, officials said.
“The emergency facilities of hospitals are on high alert and medical staff are receiving many people who have been injured in the storm. The causes of the injuries range from a fall, car accidents, objects falling on victims and injuries caused in the floods,” Oman TV said.
Swathi Suresh, a 28-year-old resident of Muscat, told The National the Omani authorities were much better prepared than they were before the 2007 Gonu cyclone — an extremely powerful storm that became the strongest cyclone on record in the Arabian Sea.
“The evacuation procedures were smooth. Timely updates and protocols also were implemented well,” she said. “Lots of relief centres and shelters popped up. Civilians are helping out too.”
Tourist resort of Muttrah hit hard by extreme weather
The popular tourist seafront town of Muttrah is one of the worst-affected areas so far.
Police have urged people living or holidaying there to flee to shelters set up by rescue services.
Omani television said about 120 people had been moved to shelters in the past 12 hours, with some flown by helicopter from their flooded homes.
“The roads in Muttrah are completely flooded with seawater and water which has moved into the shops. Cars are stranded and my cousin spent the whole night in his vehicle because the road was completely blocked with water,” Mohammed Ali Dharamsi, an Indian shopkeeper in Muttah, told The National.
The government has suspended bus services, closed seafront areas and asked all businesses to close until further notice.
Witnesses said wadis have overflowed, causing extensive damage to residential areas.
“Cars parked on the streets are covered with rain water, two electricity poles are down and the whole street has no lights. We called the emergency services but it is difficult for them to recover electricity because the rain has not stopped,” Said Al Hinawi, a resident of Barkah in the Batnah region, told The National.
Dozens more were evacuated from the flowing wadis in Sohar as strong currents swept away almost everything in their path.
“Our labour camp is gone. The police evacuated us to shelters at two in the morning. We have lost all our possessions when the wadi water came in flooding our camp,” Shaji Rajpur, an Indian construction worker in Sohar, told The National.
The health ministry has put the country on national alert, preparing all hospitals and medical workers for the worst-case scenario.
“The Ministry of Health has completed all the preparedness procedures of all health institutions to deal with the tropical conditions,” it said. “All our hospitals, clinics and medical workers are on high alert to deal with emergency situations.”