Hundreds of asylum seekers may now face deportation after missing a deadline to apply for protection visas, according to data from the Department of Immigration.

Asylum seekers who came to Australia by boat between 2008 and 2013 and have not yet applied for a visa will now be cut off from welfare payments and are expected to leave the country, now that the government’s October 1 deadline has passed.

Those who do not leave voluntarily now "risk being detained and removed from Australia," a notice on the department’s website reads.

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"You might have to pay the Australian Government for the cost of removing you from Australia."

The government will release the exact number who missed the deadline on Monday.

But an Immigration Department report from September 27, four days before the deadline, said there were 531 who had not yet applied for visas.

Of those, 235 were from Iran. The rest were from a range of Middle Eastern, South Asian and African nations – including Sri Lanka, Iraq and Vietnam.

Immigration minister Peter Dutton announced the deadline in May.

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He said it was time for the asylum seekers, who were part of a larger group of around 50,000 so-called Illegal Maritime Arrivals who landed in the previous Labor government, either proved their refugee claims or left Australia.

"We are not going to allow, given the level of debt that our country is in, for more debt to be run up paying for welfare services, for people who are not genuine," Mr Dutton said at the time.

The department said the cost of supporting the remaining asylum seekers was $1.9 billion in the 2015-16 financial year.

Immigration lawyers have been assisting asylum seekers with their paperwork on a pro-bono basis and said there had been extreme waiting lists in the lead-up to the deadline.

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“We went from having 25 appointments a week to 125,” Sarah Dale, an immigration lawyer at the Refugee Advice and Casework Service, told SBS World News.

The vast majority who did make the deadline will now wait to hear back from the department, and could be called in for further interviews.

Lawyers estimate it could be six to 12 months before their refugee status is determined.

“It's not all over. We still have heaps of work to do, there are still going to be thousands of people in the community left waiting, left wondering, left still in a state of limbo,” Ms Dale said.