“We ask only for your prayers and well wishes,” his spokesperson said.
The 64-year-old dancer confirmed that he is recovering from the surgery which was ordered after he was diagnosed with an unspecified type of cancer at Christmas.
A spokesperson for Mr Flatley - who has been an ardent lifelong supporter of cancer charities - said he was now recovering from the treatment.
"Michael Flatley has been diagnosed with an aggressive form of cancer," they confirmed.
"He has undergone surgery and is in the care of an excellent team of doctors. No further comments will be made at this time. We ask only for your prayers and well wishes. Thank you."
The dancer's current location was not specified.
It is unclear if the diagnosis of an aggressive form of cancer is linked to his treatment a number of years ago for skin cancer.
The Chicago-born star confirmed two years ago that he was treated in 2003 for a malignant melanoma.
"It was purely by chance that it was noticed," he explained to The Irish Independent.
"I had never even noticed it...it can be a frightening place to be."
Mr Flatley has homes in Ireland, the UK, US, France and Barbados - though he spends most of his time in France and the UK where his entertainment empire is now based.
It is understood he is recuperating from the surgery with his wife, Niamh, and son, Michael Jnr.
Over 15 years ago, the star was also treated for a mystery virus which left him feeling exhausted and forced him to cancel the world tour of one of his shows.
The dancer - whose parents moved to the US from Sligo and Carlow - sprang to prominence by becoming the first ever American to win the World Irish Dance Championships.
He performed with The Chieftains on tour for a number of years before enjoying a global breakthrough with a starring role in 'Riverdance', a smash-hit show which he helped to choreograph in 1993/94.
After leaving 'Riverdance', he scripted his own show 'Lord of the Dance' which, over two and a half decades later, is still touring to sell out audiences worldwide.
A major performance of the show is scheduled for Ireland this summer.
Mr Flatley also designed other smash-hit shows including 'Feet of Flames' and 'Celtic Tiger'.
His dance shows have been performed in more than 60 countries to more than 60 million people.
Estimated gross receipts for the shows worldwide are believed to exceed €1bn.
Last year he released his long-delayed spy thriller film, 'Blackbird', which he described as his homage to the golden era of Hollywood.
He has been hailed as the outstanding dance star of his generation and has performed for world leaders at the G8 summit and at Presidential inaugurations.
The star - who turns 65 years old next July - has also received multiple artistic and cultural awards as well as accolades for his extensive charity work.
Over recent years he has focused his charitable fundraising on groups that work with the homeless and agencies involved in cancer treatment and research.
For his charity work he was honoured at the Red Cross charity ball by the late Prince Rainier in Monaco.
He was also honoured by the Governor of Nevada for the record box office receipts his long-standing 'Lord of the Dance' residency enjoyed at the Venetian Casino in Las Vegas.
Mr Flatley bought the near derelict Castlehyde estate in Fermoy, Co Cork in 2001 for €3m and lavished over €27m in bringing the picturesque River Blackwater property back to its 18th Century grandeur.
He specifically chose Castlehyde as the venue for his 2006 marriage to his Meath-born wife, Niamh, who is also a dancer.
His renovation of the Fermoy property was hailed as the greatest privately funded restoration in Ireland for decades.