The officials said security forces fired bullets during the protests across the Sidama region.
Activists from the Sidama ethnic group were set to declare their own federal state on Thursday.
They accused the government of failing to hold a promised referendum on the issue.
The Sidama are Ethiopia's fifth biggest ethnic group, making up 4% of the population. The four bigger communities all have their own regions within Ethiopia's ethnically based federal system.
Reports from activists and opposition groups cite a higher death toll with fatalities as high as 60, but the local acting security head Andinet Ashenafi warns against what he called exaggerated numbers, reports the BBC's Kalkidan Yibeltal from Addis Ababa.
Mr Andinet confirmed to the BBC that four people were killed in the city of Hawassa and 26 others sustained wounds.
Members of other ethnic groups were also killed after being attacked by angry mobs.
Local media reported that protesters attacked a tourist lodge, leading to 12 tourists being escorted out by troops.
The internet has been blocked in parts of the south of the country since Thursday, including the main city of Hawassa.
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