Two-thirds of the West African state's 21-member team applied for asylum after disappearing from the athletes' village in Melbourne in March.
One said he feared being killed if he returned to Sierra Leone, devastated by a 1991-2002 civil war.
They were initially granted bridging visas but 10 have now been given permanent visas.
Sierra Leone's Information Minister, Septimus Kaikai, told Reuters that the decision by the Australian government was “most unwelcome”.
“We see such an act as exploiting young athletes from developing countries," he said. "It says to other athletes to follow the behaviour of the 10 now granted visas by putting their motherland to shame in favour of greener pastures.”
Sierra Leone is recovering from more than a decade of conflict but Freetown's streets are still full of unemployed young men, many of them former fighters.
In March, Prime Minister John Howard warned Canberra would not give widespread asylum to athletes who went missing from visiting sports teams.