Michael Ertel, who had only held the role for three weeks, stepped down after images thought to been taken in 2005 were published by the Tallahassee Democrat newspaper.
Photographs show the Republican wearing blackface, a headscarf, large earrings and fake breasts, alongside a t-shirt which has the words “Katrina victim” written on it.
The party likely took place around two months after the disaster, which killed more than 1,800 people. Most fatalities occurred in the majority-black city of New Orleans in Louisiana.
Mr Ertel had been serving as the supervisor of elections in Seminole County in 2005 – a role he held until this month when he was promoted to secretary of state by Florida governor Ron DeSantis.
“There's nothing I can say,” Mr Ertel told the Tallahassee Democrat upon being shown the photographs, refusing to comment other than to say he was the man pictured.
He submitted a letter of resignation to the governor a matter of hours later, before also deleting his Twitter account.
Addressing a press conference called to discuss the state’s response to Hurricane Michael, Mr DeSantis said he believed Mr Ertel regretted the incident.
“It’s unfortunate, I think he’s done a lot of good work,” he told reporters in Marianna on Thursday.
“But, at the same time, I’ve got to have an administration that is focused on what matters to Floridians and I don’t want to get mired into side-controversies.
“I felt it was best to just accept the resignation and move on, it is unfortunate, I think he regrets that whole thing 15 years ago, but at the same time I want people to be able to lead and not have any of these things swirling around them.”
The controversy comes weeks after Mr DeSantis narrowly won a bruising gubernatorial election, during which his campaign was dogged by accusations of racism.
The former congressman came under fire after urging Floridians not to “monkey this up”, by voting for his opponent Andrew Gillum, the first black candidate for governor in the state’s history.
The final weeks of his campaign focussed on telling voters Mr Gillum was “hostile” towards law enforcement, considered by some to be a dog-whistle reference to the debate over police brutality towards black men.
Mr DeSantis denied accusations of racism, but refused to apologise for his remarks.
“I’m not calling Mr DeSantis a racist,” Mr Gillum had commented during the campaingn. “I’m simply saying the racists believe he’s a racist.”
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