The department says its doctors are not trained to detect or treat some diseases which appear among African refugees and asylum-seekers.
The New South Wales Health Minister, John Hatzistergos, says the problems detected include tuberculosis, intestinal parasites, hepatitis, measles, rickets and malaria.
Mr Hatzistergos says while the risk to the Australia's health system is small, it does exist.
"Many of these diseases are unique and they are often of a strain that we are not familiar with, and for that reason we (NSW) have had to establish specialised services to be able to deal with them.
"It is important to recognise while some of these diseases are potentially infectious, our standards of hyghiene in this country are very high and for that reason the risks are relatively small."
Mr Hatzistergos has written to the federal Health Minister seeking more specialised healthcare support, including some Medicare assistance, for African refugees.