On the same day he accepted a trophy for his fifth Sydney premiership, trainer Chris Waller found himself embroiled in controversy over the scratching of a horse at Rosehill.

Waller was called to a stewards' inquiry into the decision to accept with Sir Mako in Saturday's 1900m race at Rosehill and then send him to Melbourne instead.

Sir Mako had 60.5kg at Rosehill but carried 56kg in a 2500m race at Moonee Valley.

The trainer denied he had tried to manipulate the weights to favour Marenostro, his other runner in the Sydney race.

Marenostro, who carried 57kg, finished fourth in the Rosehill race as the $2.10 favourite.

"With so many stayers in your stable when you make such an early decision to scratch it's going to attract some criticism," chief steward Ray Murrihy said.

"If we were of the view you put the horse in to affect the weights that would be another matter."

After two winners at Rosehill, Waller said he was disappointed there had to be an inquiry.

"I'm disappointed but I fully support the stewards and if they receive a complaint they have to take action on it," Waller said.

"I have nothing to hide.

"I've sent six horses to Melbourne and I'm lucky I have a stable there and can do it.

"I shouldn't have to be sending six horses to Melbourne because there are no races here for them.

"I'd prefer to have them racing in Sydney."

Waller ended the Rosehill meeting with two winners, Japonisme and Berrimilla and had one at Moonee Valley with Bagman.

But Sir Mako could only manage seventh in the race won by Crafty Cruiser.