The death toll from Cyclone Gonu rose to 61 with dozens of others still missing.
Residents of deep southern Iran reported massive devastation in some small desert villages, with one man saying every house in his hometown had been swept away by floods.
"Twelve people have been killed and nine injured as a result of Cyclone Gonu battering southern Iran," Farzad Panahi, the head of National Emergency Relief Committee, said on state radio. He did not provide details.
Iranian officials had reported three previous deaths, with one person killed in a car crash due to low visibility and two government workers drowned in a truck overturned by floodwaters. The 12 total figure appeared to include those three.
The storm killed at least 49 in Oman with more than two dozen others missing and feared dead.
In Iran, the floodwaters drove out the residents of Shahrestan and Kahir villages, both near the port city of Chabahar, according to state radio.
A Kahir resident said the whole village was washed away by the floods.
"Some 120 families lived here. Not a single house is standing now. People have no refuge to seek protection," he said.
"There is no water, no electricity and no food," the man said as he burst into tears. "No help has reached us."
Pahani said relief operations had started Friday as the storm subsided. He said rescue teams were using helicopters and trucks to send supplies to those affected by the storm.
Hormozgan Province Governor Saheb Mohammadi said almost all roads destroyed by the storm have reopened excluding one road connecting southern Iran to eastern Iran.
"The storm is over. The sea is calm. Excluding one road, all roads have reopened," Mohammadi said on state-run TV.
Iranian officials previously said water had encircled more than 100 villages deep in Kerman Province, where many residents subsist on livestock and small farm plots in villages consisting of a handful of families.
Video footage showed people taking their belongings to higher ground, and said hundreds were living in tents in the port town of Konarak. It also said regular flights to the town's airport had restarted.
In Bandar Abbas, Iran's main non-oil port, some people were living in school auditoriums, where they moved during the storm, the report said.
Gonu tore through the coast of Oman and southeastern Iran on Wednesday and Thursday. At the height of the storm in Oman, winds swept up to 95 mph (153 kph), according to the U.S. military's Joint Typhoon Warning Center. But the storm was later downgraded to a tropical depression and later a high-pressure system with rain and wind.
The storm spared the region's oil installations, and oil futures fell Friday on a wave of profit-taking that followed a surge in prices a day earlier. News that Cyclone Gonu had spared major oil installations in the Gulf of Oman also alleviated supply concerns.
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