Hey Doc has survived a protest to win the Manikato Stakes at Moonee Valley with the well-supported Chautauqua a late scratching by the vet.

The Tony McEvoy-trained four-year-old Hey Doc was a surprise leader in Friday night's Group One sprint and held off a late challenge from In Her Time.

Corey Brown, rider of the runner-up, fired in a protest alleging interference from the winner at the 1000m mark of the 1200m race.

Brown claimed the interference, where In Her Time was bumped by the $2 favourite Vega Magic who had pressure from Hey Doc who was crossing, had resulted in the mare being unable to lead.

In dismissing the protest, chief steward Terry Bailey said it was the opinion of the panel, interference or no interference, Hey Doc would have led the race.

Ridden by Luke Currie, Hey Doc ($21) scored by a head from In Her Time ($7.50) with Malaguerra ($21) a neck away third.

McEvoy decided to switch Hey Doc back to sprinting after his fading 10th in the Makybe Diva Stakes (1600m) at Flemington last month.

The trainer was surprised to see Hey Doc lead although it was the plan to race in a forward position.

"He began very well and Luke was caught out on a bit of a limb so he pressed on, trusted his horse and the result is fabulous," McEvoy said.

"We thought he was a Group One horse but we were a bit confused by him in the mile race so we decided to come back to sprinting and it's come off for us.

"He's now unbeaten here and he's shown he's also effective up the straight at Flemington, so we'll press on to the Darley now."

The Group One Darley Classic (1200m) is run at Flemington on November 11.

Craig Williams said Vega Magic, who finished fifth, didn't begin as he normally can and didn't appear suited racing under lights for the first time.

Chautauqua attempt at a second victory in the Group One race he won in 2015 was thwarted when he got a hind leg up on a partition in the barriers.

There was confusion when he was announced as a runner a few seconds before being declared a non-runner.

Senior trainer John Hawkes and jockey Dwayne Dunn offered a stern 'no comment' when asked their thoughts on the scratching.