Aidan O'Brien was speaking at Leopardstown on Sunday and revealed Luxembourg would not take part at Epsom.
The horse - which won the Futurity Trophy at Doncaster last season - is believed to be out of action for up to six weeks.
O'Brien found Luxembourg to be slightly lame on his off-hind following a routine canter and carried out tests over the weekend to find out the full extent of the problem.
Speaking at Leopardstown on Sunday, O'Brien said: "Luxembourg won't run in the Derby. He has to have a month or six weeks of box rest.
"It's a muscular problem behind and the tests revealed that he had to have a month or six weeks box rest to let it heal and do the right thing by the horse.
"Hopefully he'll be back for the autumn, that's the plan anyway.
"Sometimes with muscular (issues) you can keep going, and sometimes you can't. Rest was the only cure for it."
O'Brien still has the Derby favourite Stone Age who won at Leopardstown just before Luxembourg was confirmed to be missing the event.
The further Stone Age went the better he looked and the winning margin of five and a half lengths emphasises his superiority.
O'Brien - who won the race for the 15th time - was delighted with the performance.
O'Brien said: "He's lovely, he's a high cruiser, he's tactical and he keeps going - he keeps pushing it out.
"He came forward lovely and we thought he'd come forward a bit more from today. The plan was to give him two runs and because he was a maiden he started in Navan and then came here.
"We always felt he was very good and we weren't really worrying about winning a maiden (last year).
"He ran over seven furlongs in a Group One - he's a high tempo horse."
The Ballydoyle handler does not expect the demands of Epsom or the step up to a mile and a half to trouble Stone Age.
He added: "We didn't think it (Epsom) would be a problem. His two runs this year were left-handed. He usually steps quick out of the gate, he's a high cruiser and he's very happy to get a lead, which he was going to do today if someone was going to take him.
"He has that class, he's able to pick up and then he pushes it out all the way to the line. He never looks, in any of his races, to be getting weak at the line.
"He's a big hardy horse, he's not a wimp now."
When asked about assessing the pecking order of his Derby trial winners, he said: "It's impossible really. They were running in their trials individually to see what was going to happen.
"Because all the races were at different times they were all on different work schedules.
"Ryan will talk to the lads (owners) and hopefully they'll come up with a solution to the whole thing. That's usually what happens.
"You'd have to be very happy, any of the ones that had two runs they came forward from their first to their second. We thought this fella would come forward again.
"This horse has plenty of pace. Every day he has run he's always going to the line. He never seems to be stopping, he keeps pushing it out to the line."