The Department of Immigration and Border Protection has suffered a $100-million blowout in the cost of detaining asylum seekers offshore.

Detention on Nauru and Manus Island cost taxpayers more than $1 billion in the 2014-15 financial year, the sixth year running that spending has gone over budget.

Funding allocated for the period was lower than the previous year, according to the Immigration Department's annual report, though 2013-14 also saw an $89-million overspend to total $3.1 billion.

The department said the spending was attributable to a range of "minor factors", such as "higher occupancy levels than budgeted, more accurate depreciation assumptions for offshore infrastructure and minor expenditure items which were not planned", but excluding incidents recorded at the two centres over the 12-month period.

Further clarification was requested of the department, but denied.

Costs for the onshore management of what the department calls illegal maritime arrivals (IMAs) came in 16 per cent under budget with savings of more than $320 million.

The department said the closure of onshore centres did not have an impact on the offshore budget, and there were no plans to reopen any.

The annual report also recorded a dramatic decrease in the number of protection visas approved for asylum seekers arriving by boat, down 99.9 per cent from two years ago.

One protection visa was approved in the past financial year — granted to a Pakistani asylum seeker — though 2,746 were granted to asylum seekers who had not arrived by boat.

"This is due to changing government policies, including the commitment to not grant a permanent visa to an IMA," the department said.

The report also provided a breakdown of people taken into immigration detention over the 12-month period.

As of June 30 this year, 3,202 people remained in immigration detention. A total of 2,239 were described as IMAs.