Second emergency Harbour Views has been scratched from the Ballarat Cup after trainer Matthew Williams noticed some inflammation around his fetlock joints.

While it looked unlikely Harbour Views would gain a start in Saturday's Listed race, Williams was taking no chances with the lightly raced five-year-old.

Harbours Views was the $3.30 favourite before his scratching.

Williams said on Friday, Harbour Views was already in the paddock and would be checked over in early January to see whether he could begin an autumn campaign.

"It's nothing major but you don't want a change like that going into a 2000-metre race where you are probably going to hit a good three track later in the day," Williams said.

"He could be pulling up a bit messy if he did run. That's on the proviso he was to get a run.

"So we've taken the temptation away and he's gone to the paddock this morning and is already on the grass."

Williams said X-rays taken of Harbour Views' joints came back clear of any bone chips.

Harbour Views was successful at his first five starts before being beaten in the Melbourne Cup Carnival Country Final at Flemington on November 7.

Williams was looking forward to testing Harbours Views at 2000m on Saturday with a view to targeting the Caulfield and Melbourne Cups next year.

"I've always thought of him being 12 months behind," Williams said.

"We're hopeful that he will condition up and get a bit more development in his bone structure.

"We haven't got him out to 2000 metres yet which was one box we were looking to tick on Saturday.

"He switches off beautifully and you think he would have no problems running a trip like that, but until you do it, you don't know."