He said he fears the temporary accommodation could become permanent and says he doesn't want run-down mobile homes parked all over town.
Angry residents met on Saturday night and called for Mr Sciott's removal from office.
One resident, James Ruston, said his house was knocked off its foundation by the tornadoes that blasted through the town last month and is still uninhabitable.
He thought help had finally arrived when a truck pulled up to his property with a mobile home from FEMA.
Then he was informed of the ban on single-wide mobile homes.
Mr Ruston and many others see the city's decision as a sign that leaders don't care that some people are barely surviving in the rubble.
Felicia Boston, standing on a debris-strewn plot where a friend lost his home in the tornado, said: 'People have to live somewhere. What's it matter if it's in a trailer?'
Mr Scott, however, has heard all the complaints but is unrepentant.
He said: 'I don't feel guilty. I can look anyone in the eye.'
Blue-collar Cordova has a population of about 2,000 and is 35 miles north west of Birmingham.
It was hit by a pair of powerful tornadoes on April 27, the day twisters killed more than 300 people across the South east.
Officials say 238 died in Alabama, the highest death toll for any state in a spring of violent weather, the Associated Press reports.
An EF-3 tornado with winds of at least 140mph walloped the town around 5.30am, knocking out power and damaging numerous buildings.
An EF-4 with winds around 170mph struck about 12 hours later, killing four people and cutting a path of destruction a half-mile wide through Cordova.
On Main Street, virtually every storefront was destroyed and is now deserted, blocked by a chain-link fence.
Scores of homes, businesses and city buildings were destroyed.
The Cordova Police Department, a pharmacy, a bank and City Hall all have moved into similar trailers since the storm.
The law is the law, he said, and a tornado isn't any reason to change it.
At Saturday night's meeting resident Harvey Hastings said: 'There are trailers all over here but Scott wants to clean all the trash out. He doesn't like lower-class people.'
He accused the city of double standards over it decision to the local authorities to use trailers but not residents.
The mayor said: 'It's temporary and we know it's temporary. We're trying to provide services for everyone.'