Johnny Murtagh's contract as retained rider for the owner's Irish-trained horses has been terminated, according to the Aga Khan's Irish stud farm manager, Pat Downes.
The 42-year-old has ridden numerous Group One winners for the influential owner-breeder, notably guiding Sinndar to victory in the Epsom Derby, the Irish Derby and the Prix de l'Arc de Triomphe in 2000 when stable jockey to John Oxx.
Downes said: "I can confirm it (Murtagh's departure) is true.
"I don't have a whole lot more to say, other than there were differences between the parties and it was agreed that we would part."
Following Murtagh's resignation as stable jockey for Coolmore at the end of 2010, he was offered a role with the Aga Khan for a second time in November of that year.
Murtagh won the French Oaks in the Aga Khan's green and red silks aboard the ill-fated Valyra this June.
During his previous spell with Oxx, Murtagh rode 18 Group One winners for the Aga Khan.
At the time of his second stint with the Aga Khan, the jockey said: "I am thrilled to be renewing my association with His Highness' horses in Ireland.
"We have shared some fantastic moments over the years and I have always enjoyed riding in the green and red colours.
"This will also give me an opportunity to ride for John Oxx again.
"I started off riding for Mr Oxx and it has always been a pleasure to be part of his Currabeg team."
The Aga Khan announced on Monday Christophe Lemaire had penned a contract to remain as his jockey in France until the end of 2013.
In the last couple of weeks, Lemaire has won the Secretariat Stakes and the Yorkshire Oaks in his silks.
At the time of Murtagh's reappointment, the Aga Khan said: "We have had some wonderful days in the past and we look forward to renewing our successful association.
"I believe it is vital to the continued success of my bloodstock operation to have a retained jockey in the countries where my horses are trained.
"This has been the situation in France for many years and I am most pleased now to have a similar arrangement in Ireland."
Murtagh is currently injured after sustaining a hairline fracture to a small bone under an eye when kicked by his mount, Lottie Dod, in the preliminaries before the Phoenix Stakes at the Curragh on 12 August.
The jockey has ridden 46 winners so far this year in Ireland and five of his top six money-earners have been Oxx-trained Aga Khan horses, such as Takar and Sharestan, while he has won minor races on horses for the owner's other Irish trainer, Michael Halford.
Murtagh has been on hand to land some of the big British prizes, teaming up with Oxx's Saddler's Rock, who is owned by Michael O'Flynn, in the Goodwood Cup and taking the King Edward VII Stakes at Royal Ascot on the Sir Henry Cecil-trained Thomas Chippendale.
A statement issued by Murtagh read: "I was informed yesterday afternoon that my contract to ride for His Highness the Aga Khan was being terminated with immediate effect.
"I would like to take this opportunity to thank His Highness and his staff at his studs in Ireland and France for the very successful years we have had together, and to sincerely wish them every success in the future."