"When those operations have been concluded and there is no further risk to life, Border Protection Command will endeavour to recover, where possible, any bodies which may be relocated."
The spokeswoman added that the likelihood of successful recovery would diminish over time.
Asked whether the bodies would eventually be recovered, the spokeswoman said she was "not sure".
"Where it is possible, of course we will endeavour to locate and recover the bodies," she said.
"But at this stage, I don't have a timeframe on that."
Border protection commander Rear Admiral David Johnston told reporters on Sunday the focus was on finding people alive and the recovery of bodies was complex and time consuming.
The navy boat sent to look for survivors was later redirected to look for another vessel that had called for help.
More than 11,000 asylum seekers on 167 boats have arrived this year.
- AAP