A decision is likely today once the Ballydoyle trainer has discussed the situation with owners John Magnier and Michael Tabor.
“The ground is heavy and very deep. He’s in now, but he has to be a doubt,” said O’Brien.
“It’s far from ideal and will be totally against him, but knowing the horse he is, the lads might let him run.
“We’ll talk about it tomorrow and make a decision.”
However, the likely testing conditions have not dampened the spirit of jockey Johnny Murtagh should Duke Of Marmalade take on New Approach.
“I always say a good horse can go on any ground. I am a great believer in my horse, he’s tough and he’s genuine. Every time he goes he’s ready to give you 110%,” said Murtagh.
“It’s a very exciting race and I’m looking forward to it. It’s a clash of the titans and the best horse will win on the day.
“As I have said before, he’s a horse that will die for you. He can overcome difficulties and this is one thing that might not be in his favour.
“It’s a very hot race, I respect them all but fear nothing in the race,” the jockey told At The Races.
York clerk of the course William Derby is hoping the worst of the weather is behind them following Saturday night’s downpour.
“We are now heavy after 25 millimetres of rain overnight. The forecast was for it to stop on Sunday morning and it has with dry weather through the day before a band of light showers moves in later tonight,” he said.
“It looks brighter for later in the week looking at the long-range forecast and we could do with some summer.
“We’ll just take what God throws us and look forward to some good racing.”
The feature race on the opening day of the Ebor Festival is being described as the race of the season after Duke Of Marmalade, unbeaten in four Group Ones this year and Derby winner New Approach were among 11 declarations.
New Approach, trained by Jim Bolger, has been sidelined with a muscle problem since winning the Vodafone Derby 10 weeks ago.
However, the gamble on New Approach continued with Coral forced to cut him again to 5-2 from 11-4 having been 3-1 on Sunday morning.
“Some seriously shrewd punters have been backing New Approach which suggests he will be ready to run to his very best at York on Tuesday,” said Coral spokesman Simon Clare.
Stubbs Art, who finished one place behind New Approach when third in both the English and Irish 2000 Guineas, is expected to benefit from a step up in trip but that could be counteracted by the testing ground.
“On that ground I would prefer it to be a mile as it’s going to be pretty testing,” said Jimmy Lindley, racing manager to owner Matthew Green.
“He’ll get a mile and a quarter but it will be more like a mile and a half so we are jumping up stamina wise and guessing a bit.
“The trainer thinks he’ll run up to his Guineas form which means we’ll give the Derby winner a run to the line and David (Elsworth) is never one to go down without a fight.
“It’s his first run since Ascot and he’s working well. He did a bit of work the other day and came through it fine. It wasn’t a serious gallop but he did it well.”
John Gosden has declared Pipedreamer, a recent course and distance winner, but warned he will only run if the ground is suitable.
Juddmonte International betting
Coral: 4-5 Duke Of Marmalade, 5-2 New Approach, 7-1 Phoenix Tower, 10-1 Pipedreamer, 14-1 Linngari, 16-1 Multidimensional, 50-1 Halicarnassus, Rob Roy, 66-1 Championship Point, Red Rock Canyon, Stubbs Art.