Lawyers for Mr Craig denied the charges before they were filed.
The charges against Mr Craig claim he lied to federal prosecutors in the Department of Justice about his foreign lobbying efforts and concealed information about his private work in Ukraine for the Russian-backed government.
If convicted, he could face a maximum of five years in jail for each count along with over $250,000 (£191,000) in fines.
Under US law, all lobbyists for foreign governments must register with the department.
Mr Craig’s work in the Ukraine happened after his year-long tenure with the Obama administration, while he was a senior partner at the Skadden, Arps, Slate, Meagher & Flom law firm.His 2012 project in Ukraine was allegedly a part of Manafort’s illegal lobbying efforts.