Many of the 1378 staffers who joined DFAT when the departments merged in late 2013 may be forced to wait until the end of 2016 for their clearances to be upgraded.

The integration of the two departments created a backlog of applications with the average wait for a department standard clearance now six to eight weeks.

DFAT requires ongoing staff in Australia or on long-term overseas postings to have negative vetting two clearance – formerly known as top secret clearances.

The department has recognised the negative one clearances formerly held by AusAID staff, which allow them to perform certain duties until they are upgraded.

"All former AusAID staff have a level of clearance that enables them to work in DFAT," said a department spokesman. "We expect all former AusAID staff to be upgraded by late 2016."

The department has prioritised the applications of staff selected for long-term overseas posting or promotions.

One negative vetting two clearance costs taxpayers close to $2000 on average although DFAT may have reduced this cost given AusAID staff already had already completed background checks.

"All 2015 graduates have been security cleared," the spokesman said. "The security clearance process for the 2016 graduate intake is well underway and we expect all graduate clearances to be finalised prior to the start of the 2016 graduate program."

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Graduate intake at DFAT will remain relatively stable this year with the department recruiting for 46 positions compared to 40 in 2015.

Almost all of the Australian Public Service's 10 biggest employers have hired more grads for the coming year than in 2015 when graduate ranks slipped to the lowest level in a decade.

The Department of Defence is set to significantly boost its graduate ranks with offers sent to 250 applicants. In 2015, the department hired 161 graduates although not all have received security clearances.

"Approximately 98 percent of security clearances for 2015 Defence graduate program participants have been finalised," a Department of Defence spokesman said.

Security clearances for slightly more than half of the 2016 defence graduates have been processed, with the majority expected to be completed before they begin work in coming weeks.

Defence would not disclose the number of staff with active clearances at each level, although 70 per cent of the 350,000 security clearances managed on behalf of the Australian government are from defence.

Average security clearance processing timeframes have increased by approximately 12 percent within the department since 2014/15.

"Higher clearance levels require more checking and rigour, in accordance with the Australian Government Protective Security Policy Framework," a department spokeswoman said. "Consequently, suitability assessments at the higher clearance levels take longer to complete."

The current waiting time for a positive vetting security clearance at defence is 13.5 months, while staff will need to wait 6.2 months for a negative vetting two clearance or five months for a negative vetting one clearance. A baseline clearance is granted in less than one month.