Richard Hannon's Strong Suit will undergo a breathing operation following his disappointing run in the Greenham behind Frankel.
The betting suggested he was the only colt capable of giving Henry Cecil's superstar a race yet he trailed home last of the six runners.
The son of Rahy is without a win since landing the Coventry Stakes in last-gasp fashion.
"I know that Strong Suit is a good horse, so something had to be wrong for him to run so badly at Newbury," said Hannon.
"The initial scope showed nothing abnormal, but we then checked his wind and found that he could barely breathe.
"There are various degrees of wind operations, but Strong Suit will have the 'Full Monty', and hopefully he will bounce back as good as new.
"He will definitely be off games for two months, so there is no chance of getting him back in time for Royal Ascot but Julie Wood, the colt's owner, has told me to give the horse all the time that he needs and with luck he'll be back on the track some time in July.
"Richard (Hughes) is adamant that we have not seen the real Strong Suit since he won the Coventry Stakes so impressively at Royal Ascot last year, so maybe the problem has been there some time and gradually got worse, but at least now we know there was a reason for his below-par performance at Newbury," he told richardhannonracing.tv.
