Unbeaten Black Caviar was on Sunday night diagnosed with two muscle tears and severe bruising to her hind quarters after her famous win in the Diamond Jubilee Stakes at Royal Ascot.
Veterinarians told trainer Peter Moody "she would have definitely felt it during the run".
"She's had something like this before," Moody told the Herald Sun yesterday, adding he did not know when she might have picked up the injuries.
"She's entering quarantine today, we're sending her home, but we'll be able to have the injuries treated whilst she's in quarantine."
Vets inspected the unbeaten mare at her Newmarket stable base and located the muscle injury and bruising.
The physical issues could explain why her customary acceleration and speed were missing during the Diamond Jubilee Stakes.
The Wonder From Down Under was still poised to register another comfortable win when jockey Luke Nolen controversially dropped his hands near the line, almost costing the mare her unbeaten record.
Given the vagaries of travel, Nolen's riding blunder and the injuries the mare sustained during the race, the Diamond Jubilee Stakes may now go down as one of the greatest of her 22 wins.
Moody said Black Caviar ate up after her Royal Ascot win but said she was "very flat and tired" yesterday morning.
Moody said no decision on Black Caviar's racing future would be made until the mare had returned to Australia, recovered from her injuries and enjoyed a deserved spell.
Moody is still hopeful Black Caviar will race in Melbourne during the spring carnival.
Caviar, the 1/6 ($1.16) favourite scrambled in by only a head from French mare Moonlight Cloud $6, with another French filly Restiadargent (40/1) a neck away third in her narrowest winning margin.
Soul, the former Sydney sprinter who would not have got near Black Caviar in Australia, finished fourth, only about a length from the great mare.
Black Caviar certainly wasn't at her supreme best but she was still able to notch the 12th group one win of her career, taking her prizemoney to more than A$6.5 million.
However, regular rider Melbourne jockey Luke Nolen would not have enjoyed his breakfast reading yesterday morning after copping a savaging by the local racing scribes for nearly costing Black Caviar her unbeaten record.
Instead of reading about Black Caviar's extraordinary achievement to win 22 races in succession in the Diamond Jubilee Stakes, Nolen became the story.
"The blunder from Down Under! Black Caviar wins despite jockey error", was the headline in Racing Post.
"Black Caviar came within a whisker of losing her unbeaten record after jockey Luke Nolen dropped his hands in the closing stages and almost allowed Moonlight Cloud to steal the race on the line," Tom Kerr wrote.
The Guardian headline said it all: "Black Caviar survives Luke Nolen blunder to win at Royal Ascot."
"Black Caviar's first race outside Australia turned into a piece of astonishing drama that thrilled 77,000 people here and millions around the world, leaving only her jockey, Luke Nolen, ashen and full of regret," wrote Chris Cook.
The Mail On Sunday's headline read: "I nearly blew it! Jockey Nolen owns up to Ascot howler."
The Sunday Mirror's headline read: "Luk-y devil: Black Caviar is a Royal Ascot winner despite jockey's error.
"Strewth! Australia's flying Sheila almost got mugged by a couple of French fillies on the final day of Royal Ascot."
However, part-owner Peter Werrett was a little kinder to his fellow countryman.
"She was probably feeling a bit sore and as soon as Luke dropped his hands, she decided she was going to stop," Werrett told Associated Press.
"I feel a bit sorry for Luke as the horse was raring to stop. I don't think there is any doubt that if he'd rode her out, she would have won by a length and a half."
We will give Werrett the final word as he put the wonderful mare's record into perspective.
"If we retire her tomorrow, she's gone out with 22 wins, with the last win being at Ascot. We've met the Queen and the horse got a pat from the Queen."