Deputy Prime Minister Barnaby Joyce's bid to move government agencies to rural towns has suffered another setback, with a majority of staff refusing to leave Canberra.

The Canberra-based Rural Industries Research and Development Corporation will relocate to Wagga Wagga within weeks, but only three staff are expected to move, including managing director John Harvey.

Deputy Prime Minister Barnaby Joyce want to see more government agencies move to the bush. Credit:James Brickwood

The small agency, which had 18 employees when the $1.4 million relocation was confirmed earlier this year, has already advertised for replacement staff for the Wagga Wagga office.

The RIRDC was one of three research bodies told in 2014 to prepare for a relocation, including the Fisheries Research and Development Corporation and the Grains Research and Development Corporation.