Chris Waller has been fined $30,000 and Junoob stripped of a Group One win after the horse returned a positive swab following his victory in the Metropolitan.

Sydney's premier trainer fronted Racing NSW stewards on Thursday after two samples taken from Junoob following his October 4 win tested positive to frusemide, a type of diuretic commonly known as Lasix.

Waller pleaded guilty to the charge and explained the substance had been inadvertently given to Junoob on race morning by a stable employee who was administering scheduled doses of frusemide to eight other horses not running at Randwick.

Racing NSW deputy chief steward Greg Rudolph described the fine as significant.

"It's probably the largest monetary penalty that's been handed down for a positive swab in NSW, if not Australia," Rudolph said.

Racing NSW had withheld payment of the $245,000 Metropolitan first prize money cheque to Junoob's connections.

With the horse disqualified, the money will go to the owners of second-past-the-post Opinion who is also trained by Waller.

The trainer advised stewards he had improved safeguards in his stable system since he was notified one of his horses had returned an irregular swab, including ensuring two staff administered routine medications to his horses.

Sydney's dominant trainer, Waller won his tenth Group One race of the year when Moriarty took out the Kingston Town Stakes in Perth last Saturday.

He has trained more than 50 Sydney winners this season and will be out to add to that tally at Randwick on Saturday with his team headed by the Villiers Stakes trio of Strawberry Boy, I'm Imposing and Multilateral.

In April last year, three Waller-trained horses tested positive to Ibuprofen - a non-steroidal anti-inflammatory treatment - as a result of contaminated feed.

The horses were disqualified from their placings but Waller wasn't punished as stewards found he was not at fault and the contamination had occurred at the feed mill.