"'Restore' may not capture the full sense of where we are. For the very hard impacted areas, I think you're in a 'rebuild' area," he told CNBC's "Squawk Box."
"That's a big deal. People need to understand this is going to take perhaps weeks, not days, in some areas," Fanning said.
Parts of northern Florida, including Jacksonville, experienced heavy flooding, which will temporarily prevent crews from accessing some areas.
Duke Energy, which serves 1.8 million customers in parts of central and northwestern Florida, is trying to restore service to 1.2 million residences and businesses.
Florida Power & Light Company, which provides power to an estimated 4.9 million accounts across the state, had about 3.5 million customers without electricity as of Monday afternoon, said Rob Gould, vice president and chief communications officer at FPL.
Counties affected by Florida Power & Light outages. Source: FPL
The initial damage assessments suggest power can be restored to parts of the state's east coast in just days, but some of the west coast will require rebuilding that could stretch out for weeks, Gould told CNBC's "Power Lunch."
"This is not a typical restoration that you're going to see. We actually for the first time in our company history have our entire 27,000-square-mile, 35-county territory under assault by Irma," he said.
FPL said it would first repair any damage to power plants, transmission lines and substations, then prioritize critical facilities such as hospitals and water treatment plants. The electricity company would then turn its attention to areas that are home to supermarkets, gas stations and other community services.
Florida utilities invested billions into their systems after devastating hurricane seasons in 2004 and 2005 in order to make them more resilient and easier to restore after a storm. Irma, which ranked among the most powerful storms in the Atlantic, has nevertheless tested those systems.
The upgrades have allowed FPL to automatically reroute power and address about 1.5 million outages, Gould said. The company strategically placed 19,500 restoration workers before the storm hit, but it cannot use bucket trucks to fix power lines until winds die down, he said.
Some parts of Florida's distribution system — the lines that deliver electricity from power plants to businesses and residences — run underground. However, the state's long coastline and the associated danger of storm surge and seawater incursion make it impractical to run lines beneath the surface in some areas.