DFAT secretary Peter Varghese told a Senate estimates hearing on Wednesday he was personally conducting a review of overseas deployments, and a decision on staffing levels would be made in coming months.

"I am currently conducting a review of staffing not in terms of reducing the numbers but in terms of whether we have got the right numbers in the right places," he told Labor Senator Anne McEwan.

"It's quite possible that review of staffing may alter the balance between staff in Australia and staff abroad, but I won't know until the review is done and we have taken decisions."

The department currently employs 3950 Australian staff with 864 officials posted in embassies and consulates across the world, most based in Asia.

Mr Varghese said the department would comply with its enterprise agreement obligations to consult staff about any changes at an appropriate time.

"I expect the review itself would be concluded within a month or so and then we have to consider what it recommends and make a decision, so I think probably within the next two-three months," he said.

Mr Varghese's review comes after the department shed 549 jobs to comply with budget requirements outlined in the 2014-15 budgets.

"That 549 can be broken down further to 465 Australia-based staff ... and 84 locally engaged staff who are the staff we recruit abroad," he said.

Mr Varghese said the 410 staff had chosen to volunteer for redundancies and no employees had been forced to leave the department.

"I made it very clear at the start of the process that we wouldn't be going down that path," he said.

DFAT officials also confirmed more than 750 former AusAID staff were still waiting for security clearances after merging with the department more than 18 months ago.

When questioned by Senator McEwan, Mr Varghese said the delays were not impacting the operations of the department despite some administrative problems.

"They would not be precluded from doing a decent day's work but there may be some documents to which they may not have access to because they don't have the relevant security clearances," he said.

"It is not ideal and I would prefer all of them had the level of security clearance we require across the board but I think we can work within the constraints we've got and I don't see any serious problem as a result."

Of 1378 former AusAID staff who went to DFAT with a clearance below negative vetting two, 330 have been upgraded and another 265 are being processed.

The security clearances of another 774 are still awaiting action and may not be completed until the end of 2016, costing the department an estimated $1.3 million.

Mr Varghese insisted the delays would not result in former AusAID employees missing out on promotion opportunities.

"In fact, we wouldn't even check on their security clearance when we consider their merits for promotion," he said.