The Federal Government will spend more than $900 million to resettle an additional 12,000 refugees fleeing Syria and Iraq.

The Department of Immigration and Border Protection has been allocated $35.2 million of the $909 million, a small part of the $1 billion overall boost in the department's budget unveiled in the Mid-Year Economic and Fiscal Outlook (MYEFO) today.

The additional expenditure comes as Treasurer Scott Morrison faces down a deficit stretching beyond the end of the decade, with a surplus now not expected until 2020-21.

MYEFO documents outlined an increased federal budget deficit of $37.4 billion, with Finance Minister Mathias Cormann citing unavoidable expenditures such as the increased refugee intake.

The resettlement funding will be spread across nine government departments, with the Department of Social Services taking the majority at $638.1 million over four years.

The Health and Education departments have also been allocated significant funding of $61.2 million and $93 million respectively across a four-year period.

The Government also allocated $44 million to provide food, water, healthcare and education to people displaced in the Syrian and Iraqi conflict zones.

In Australia, the Department of Immigration and Border Protection has been allocated $499.7 million to manage the legacy caseload of asylum seekers.

An additional $342.2 million has been allocated over two years for refugee resettlement arrangements for asylum seekers in offshore centres, as well as $213.3 million over four years for the management of the onshore centres.