Farmer, 41, a lieutenant with the Hamilton County Sheriff's Department, said he is leaving his job of 18 years to head the expanded, 7-year-old task force.
Farmer has helped oversee the grant-funded task force since it was organized as a regional effort.
"He (Farmer) is recognized across the state and across the nation for his expertise," U.S. Attorney Russ Dedrick said in announcing the appointment Thursday.
Farmer said he will remain in Chattanooga and there will be three regional directors.
"I will be doing quite a bit of commuting," he said.
Dedrick said the task force this year is receiving $987,000 for intelligence and $2.9 million for operations from the federal government.
"I can tell you that due to the effort of Hamilton County, and the support of the sheriff's department and you, we've cut this meth scourge approximately in half," Dedrick told Hamilton County commissioners.
He said a new task force meth database is "the best model that we have in the entire nation." It cross-references information and incorporates pharmacy records of drugs used to make meth so law enforcement can identify those who have purchased excess amounts.
The task force has spent $6.85 million since 2001, records show.
Denise Hamby, the sheriff's department finance director, said there is no money left from previous grants.
County Mayor Claude Ramsey said he was grateful for the federal support.
"My fondest wish is someday we don't have these kind of conversations because the problem isn't there," Ramsey said.