He appeared in court Tuesday afternoon but did not offer a comment regarding the allegations.
"It's a shock to everybody and an embarrassment to the county," said Dr. Robert McLaurin, Franklin County Cancer Center.
Green is charged with two counts of Class C embezzlement, one count for each $100,000 that was allegedly taken. If convicted, he could get nearly 40 years in prison.
Green abruptly retired as Franklin County Sheriff in January, citing health and personal matters. Green was elected sheriff in 2006 and was re-elected in November.
Court records show Green received over $200,000 from the county for an undercover drug unit. The sheriff reportedly told the county finance director he was spending the large sums of money on a confidential and "huge" federal drug investigation involving a county commissioner and two senators.
But records show less than $30,000 went to the unit.
County auditors were asking Green to account for the missing money when he resigned and the SBI began an investigation.
According to a search warrant obtained by ABC11, Green admitted to investigators he took money.
"I took money, I'm not going to lie to ya'll. I became depressed. I wanted to stay home. I took money to buy things for the kids, clothes, gas," Green is quoted.
While he's charged with taking more than $200,000, Green admitted to only $90,000.
Earlier this month, the Franklin County Board of Commissioners named a replacement for Green.
Jerry Jones, who preceded Green at the sheriff's office, has the job again.
Green is out on bond.