A cull of kangaroos at a Department of Defence site in the Australian capital Canberra is to go ahead.

The plan to kill hundreds of eastern grey kangaroos at the Belconnen Naval Transmission Site (BNTS) was scrapped about two months ago in favour of moving the animals.

In a statement released on Friday, the department said the Australian government had decided such an option would be too expensive.

Defence spokesman Brigadier Nikolic says there is now no option but to proceed with a cull.

"We have a contractor that will undertake the cull in accordance with a humanitarian and humane treatment of kangaroos as that cull proceeds," he said.

Brigadier Nikolic says other options, including trying to limit the animals' fertility, were thorougly explored before the cull decision was taken.

"We anticipate it'll take some weeks to complete and a couple of hundred of kangaroos are planned to be culled at this stage."

The president of the Wildlife Protection Association, Pat O'Brien, says protesters are disappointed.

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