Ballots representing about 10 percent of the Hillsborough County vote were being recounted Tuesday night by election workers, who expected the process to last into the morning.
About 38,000 ballots from the final days of early voting failed to upload properly and had to be rescanned by hand, election officials said.
"The memory cards from those early-voting machines just didn't properly upload," interim Secretary of State Dawn Roberts told reporters in Tallahassee on Tuesday night. "So, again, you just take the paper ballots and rescan them through the high-speed scanners."
By 11 p.m., 22,000 of the ballots had been counted, said Travis Abercrombie, a spokesman for the Hillsborough County Supervisor of Elections.
The uncounted ballots include the early voting from Thursday through Saturday at eight places: Jan K. Platt Library in South Tampa; Elections Services Center on Falkenburg Road; West Tampa; South Shore; Upper Tampa Bay; Temple Terrace Library; New Tampa; and Town 'N Country.
About 15 to 20 election workers were assigned to feeding the ballots into working machines to be counted, he said.
Roberts could not elaborate on how the error occurred, though she said it would be investigated by Hillsborough elections officials.
"They will have to report that problem to us under Florida law," she said.
Abercrombie said the machines in question had passed service tests earlier, and the problem occurred only when election workers tried to upload the memory cards to the computer system.
"We have a staff that is working through the night, and all the machines that can be used are being used," Abercrombie said.