Kim MacPherson says in her annual report that amounts owed to the provincial government more than doubled between 2002 and 2012, increasing to $2.6 billion.
She said the amounts owing cost the province an average of $95 million a year in carrying costs.
MacPherson also found that debtors are treated differently depending on the department that holds the debt, and collection efforts have focused more on individuals.
MacPherson says anyone who owes money to the government should be treated the same.
"Collection efforts need to be a priority focus to ensure all money owed to government is collected," she said.
MacPherson said the province has taken a number of steps including working with the Canada Revenue Agency to take owed money from tax refunds.
Finance Minister Blaine Higgs said that initiative is paying off and it has seen about $22 million collected and is targeting another $120 million for collection.