The 48-year-old Chicago Democrat was in federal custody Tuesday morning, according to Bureau of Prisons spokesman Chris Burke.
Jackson's spokeswoman, Bunnie Jackson-Ransom, said Jackson reported Monday to Butner, but there was a mix-up with paperwork that delayed him checking into prison. He was accompanied by his attorney, C.K. Hoffler, and North Carolina U.S. Rep. G.K. Butterfield.
Hoffler told reporters in Atlanta Tuesday that she was contacted by Bureau of Prisons personnel and asked to pick Jackson up about two hours after dropping him off at a North Carolina prison.
The former congressman then spent Monday night at a hotel and reported to prison again Tuesday morning.
Butterfield said Jackson was in good spirits entering the prison, "all things considered."
Jackson pleaded guilty in February to conspiring to spend $750,000 in campaign funds on personal expenses.
Jackson's wife, Sandi, was sentenced to a yearlong sentence for filing false tax returns. In a concession to their two school-aged children, the judge allowed the Jacksons to stagger their sentences.
Court documents were never clear about when Jackson must report.
In her sentencing order written earlier this year, U.S. District Judge Amy Berman Jackson in Washington said he would have "to surrender for service of sentence no earlier than Nov. 1, 2013."
A Bureau of Prisons website says Jackson's inmate number is 32451-016.
Jackson used campaign money to buy a $43,350 gold-plated, men's Rolex watch and $9,587.64 on children's furniture, according to court papers filed in the case. His wife spent $5,150 on fur capes and parkas, the document said.
Jackson asked to serve his time in Alabama, while his wife's attorney said she'd prefer a Florida prison. The U.S. Bureau of Prisons decided where Jackson is serving his term.
The son of a famed civil rights leader, Jackson, a Democrat, entered Congress in 1995 and resigned last November.
Hoffler said Jackson wanted to report early to begin "paying his debt."