The Federal Court of Appeal says, despite his arguments otherwise, Black was a Canadian resident at the time and that means he owes money to the Canada Revenue Agency.
The court also said Black should pay taxes on all income earned outside the United Kingdom, not just his Canadian income.
The decision follows an appeal filed earlier this year by Black's lawyers who argued the former media baron was, for tax purposes, a resident of the United Kingdom in 2002.
In a decision last month, the appeal court dismissed the case and said Black would be responsible for related costs.
The courts did not disclose how much Black may owe in back taxes, though the government has estimated the amount of income and benefits Black owes taxes on may be as high as $5.1 million.
Black has battled with Canadian authorities over a number of issues since his release from a U.S. prison in 2012.
Still outstanding is an Ontario Securities Commission case seeking to ban Black from ever serving as a director or officer of a public company in the province.
In the United States, Black served 37 months for convictions on fraud and obstruction of justice relating to his time as the head of media giant Hollinger. An appeal court tossed out two other fraud convictions against him and against two other Hollinger executives.