The Agriculture Department is the latest federal government operation to be swamped by requests for redundancy payouts from its workers.

More than 500 of the department's public servants want out, most of them working in Agriculture's vital border protection divisions, but bosses say they can still keep the nation's bio-security safe even with drastically reduced numbers of staff.

Departmental Secretary Paul Grimes says the number of applicants far exceeds the amount of payouts on offer and that many of his department's bureaucrats will be disappointed.

The Canberra Times revealed in November that the border protection units would be the first to be targeted as the cash-strapped department tries to get its budget deficit problems under control.

Dr Grimes told staff last month that 340 of his border compliance workers, from a workforce of about 2000, had applied for golden handshakes.

The department told Senate Estimates last week that 53 redundancies had already been made this year in biosecurity with more jobs set to go from the Landcare program and other divisions.

"More than 500 EOIs [expressions of interest] were made through both phases of the program: over 340 were from phase one, the Border Compliance Division in Canberra and its passengers, mail and cargo programs in the regions, and the remainder across phase two and all employees," Dr Grimes told his department.

"These numbers are well above the number of voluntary redundancies we have been broadly planning for, but we are aware that not everyone who has submitted an expression of interest will actually want to proceed after considering their estimated package.

"Still, it looks like, overall, we may have more people interested in a VR than we can offer, mostly in Canberra.

"As a result, a great deal of work is still required to work through applications to ensure that the final allocation is as fair as we can make it and it meets our business needs."