The payout was given to Khadr on Wednesday and was cashed immediately, the report said, citing a source involved in the transaction.
Reuters reported earlier in the week that Canada's Liberal government would apologize to Khadr and pay him a compensation.
A Canadian citizen, Khadr was captured in Afghanistan in 2002 at age 15 after a firefight with US soldiers. He pleaded guilty to killing a U.S. Army medic and became the youngest inmate held at the military prison in Cuba.
Khadr later recanted and his lawyers said he had been grossly mistreated. In 2010, the Canadian Supreme Court ruled that Canada breached his rights by sending intelligence agents to interrogate him and sharing the results with the United States.
Khadr spent a decade in Guantanamo before being returned to Canada in 2012 to serve the rest of his sentence and was released in 2015.
Khadr was taken to Afghanistan by his father, an al Qaeda member, who apprenticed the boy to a group of bomb makers. The father died in a battle with Pakistani forces in 2003.