The White House says the four counties named are Brevard, Monroe, Okeechobee and St. Lucie.
The designation means state and eligible local governments in the four counties, along with certain non-profit organizations, will receive federal funding for emergency and repair work.
The government has not decided whether to extend disaster aid to homeowners whose properties were damaged by flooding or winds, the Palm Beach Post reported Monday.
A spokeswoman for emergency management in Okeechobee County said officials hope to have a decision in coming days about assistance for individual homeowners.
Fay made history with a record four landfalls in Florida, hitting Key West, the southwest coast, northeast Florida and the Panhandle.
The storm was downgraded to a depression Saturday night but its remnants were expected to drop several inches of rain in the southeast on Monday.