Onishchenko was presented with a South Ossetian passport on Wednesday during a meeting with Eduard Kokoity, the leader of the breakaway Georgian region.
According to the passport, Onishchenko is registered in a private home in the South Ossetian capital, Tskhinvali, Kokoity said, Interfax reported.
"It's true that our laws say a government official has no right to have double citizenship," Onishchenko told journalists Thursday.
"But I was given this. I didn't write a request for double citizenship," he said. "I consider it a symbol of recognition of my very modest accomplishments."
A 2006 federal law that was signed by then-President Vladimir Putin restricts foreign nationals from holding government posts.
The law mentions the federal and regional parliaments, the Security Council and the Audit Chamber, without specifically listing the Federal Consumer Protection Service, which Onishchenko heads.
After the Georgian-Russian conflict in South Ossetia last August, Onishchenko went to Tskhinvali with Russian sanitary inspectors to test local water quality and epidemiological conditions.
No country except Russia and Nicaragua recognizes South Ossetia as an independent country with valid passports.
Most South Ossetian residents have Russian passports.
"I am very proud," Onishchenko said of his new passport Thursday.
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