Johnson pleaded guilty to conspiring to misuse of federal rebuilding grants, awarded to his non-profit, toward his unsuccessful campaign for state senate in 2007.
"Your honor, I accept full responsibility for my actions and what I did," Johnson, 63, told District Judge Lance Africk in court Wednesday.
The (New Orleans) Times-Picayune reported Johnson faces a maximum of five years in prison and a $250,000 fine.
The charge is in regard to three contracts Johnson filed with the government to verify reconstruction work on his home in Eastern New Orleans under a $150,000 federal loan authorization.
In court, U.S. Attorney Jim Letten called the contracts "completely concocted, false invoices."
Johnson is the second New Orleans City Council member to resign in recent years after pleading guilty to a federal crime. In 2007, Councilman Oliver Thomas admitted to demanding illegal payments from a City Hall vendor.