The US military's Joint Typhoon Warning Centre said that the storm continued to lose steam, dropping off to tropical storm strength early on Thursday.
The centre predicted Cyclone Gonu would hit the Iranian northeast coast late on Thursday but was likely to spare Iran's offshore oil installations that lie more than 200km to the west.
Tens of thousands of Iranians who fled the worst tropical storm to hit the region in decades sought shelters on Thursday as they awaited a second round of stormy winds and heavy rainfall.
Cyclone Gonu hit Iran's southern coast late on Wednesday after arriving across the Strait of Hormuz from Oman, packing winds of 200km an hour - damaging some clay-built houses.
Officials said that over 40,000 people had been evacuated from coastal areas in the southern Sistan-Baluchestan and Hormozgan provinces to safer places.
"We are expecting the second wave in the next hours to hit the province and we are already seeing the rain," Yasser Hazbavi, the head of Hormozgan's natural disaster committee, said.
"We have evacuated the beach areas, and the situation is not back to normal yet. We are waiting for second wave which even could be more intense," he said.
"We are asking the people to remain in the sanctuaries and wait for our further announcements."
Hospitals in both provinces are on high alert to receive any casualties but it did not appear that the cyclone had caused death or severe injuries.