Pickens County Sheriff Rick Clark said he believed the lowering of the flag to half-staff was a tribute that should be reserved for U.S. citizens.
"To show a sign of respect for what Nelson Mandela's done, I have no problem with lowering it in South Africa, in their country," Clark told a local television station.
"But in our country, it should be the people, in my opinion, who have sacrificed for our country."
On Friday, the sheriff's flag flew at half-staff in honor of a South Carolina law enforcement officer who was killed in the line of duty and it remained lowered through Pearl Harbor Day on Saturday.
The flag was raised to the top of the mast on Monday, however, and the sheriff's office said Clark would have no further comment beyond what he told a local TV reporter.
Obama ordered flags to be flown at half staff until sunset Monday.
South Carolina, in the heart of the old Deep South, has a troubled history when it comes to race relations and civil rights.
Governor Nikki Haley, a Republican and daughter of Indian Sikh immigrants, posted a tribute to Mandela on her Facebook page last Thursday.
Some commentators on the Facebook page later responded by calling Mandela everything from an "evil man" and "devout Marxist" to "a socialist goon."
Sheriff Clark was far more respectful in the specific comments about Mandela he made on his own Facebook page.
"I urge you to read about President Mandela over the next few days of mourning and be inspired for public service for your community and the nation as he was," Clark wrote.
