The largest cattle agent at the biggest saleyards in Australia says the National Livestock Identification System equipment is not up to scratch and needs to be replaced.

It has been five months since Queensland's Roma saleyards spent $300,000 upgrading their facilities to cope with the new electronic ID system .

Elders agent Mick Connell says the equipment is not scanning tags properly and it is taking up to a third longer to process cattle.

"I suppose in those big sale days there it could be another two or three days hold up with cattle that don't go through the scanners, they've got to go over to the crush to be re-read," he said.

"It's costing us probably three extra staff a night to put the cattle through the scanners and deliver them up to the draft and the company has to absorb the costs at this stage of the game."

The Roma Saleyard Board has acknowledged the problems and says it is dealing with them.

Meanwhile the RSPCA says Victoria's saleyard operators need to make major improvements to their animal welfare management.

The society is concluding an investigation into Ballarat saleyard, following public complaints.

It says it is satisfied Ballarat Council has addressed many of the issues raised, including overcrowding of pens, injured animals left unattended, and animals left outside for long periods of time in extreme weather.

But the Victorian RSPCA's senior inspector, Ken Waixel is still concerned about other yards.

"Ballarat saleyards are no different to any others in fact they're most probably a bit more proactive, once we've identified the issues with them, in dealing with them," he said.

"There's no one that stands out. We actually carry out inspections of a number of saleyards. We do inspections of some more often than others because of the history of those saleyards."