Twice as many asylum seekers are in Australia for medical treatment than remain in Papua New Guinea and Nauru.
Home Affairs secretary Michael Pezzullo says 562 people remain in PNG and Nauru - about 23 per cent of peak levels in June 2014.
Another 1117 have been brought to Australia for medical treatment or to accompany family members.
Regional processing on Manus Island will be terminated at the end of November.
"The remaining transferees on Manus Island will shortly be moved to Port Moresby, with services there to be managed by the PNG government," Mr Pezullo told a Senate estimates hearing in Canberra on Monday.
Meanwhile, 632 people have been transferred to the United States under a refugee resettlement deal.
The deal was expected to accommodate up to 1250 people.
"Australian and United States officials have contacted all eligible refugees in Nauru, PNG and Australia to confirm their ongoing interest in resettlement," Mr Pezzullo said.
"The United States is working through all outstanding cases, with the intention to conclude interviews by the end of the year."
There are more than 205,000 people in Australia on bridging visas, while about 62,000 people in the country have overstayed visas.
The department spent more than $72 million on external legal expenses in the past year - an increase of more than 140 per cent over the five financial years to 2018-19.
Mr Pezzullo said the increase was "almost entirely attributable" to sustained upsurges in migration and citizenship cases, including by asylum seekers who arrived in Australia by boat.
Australia has experienced a significant growth in visa applications over the past 12 years.
Visitor visas have increased by 56 per cent to 5.7 million granted, while 405,000 student visas have been granted, a 46 per cent increase.
"Improvements in our checking and intelligence systems have led to a significant increase in the detection of high risk and fraudulent applications," Mr Pezzullo said.
The average refusal rate across the visa programs increased from 2.4 per cent to 3.9 per cent over the past five years.
Of the 40 million people granted a temporary visa over the past five years, only 88,000 applicants lodged claims for protection in Australia, which is about 0.23 per cent of the temporary visas granted.
Mr Pezzullo said his department had also made significant progress with a backlog of citizenship applications.
More than 127,000 people were granted citizenship in 2018-19, an increase of 58 per cent on the previous year.
"This is despite refusals - which take longer to process - rising by 53 per cent," Mr Pezzullo said.
The department also reduced the caseload of citizenship applications to about 164,000 from a peak of almost 248,000 in July 2018.
© AAP 2019