Princess Haya Al Hussein, 45, is claimed to have been helped by a German diplomat after fleeing Sheikh Mohammed bin Rashid Al Maktoum.
It has sparked a potential diplomatic crisis between the two countries – and the Sheik has voiced his fury in an Instagram post, accusing her of “betrayal”.
He wrote: “Go to whom you get busy with!!!!!?”
According to The Sun, the princess has taken (£31 million) to start her new life.
Unconfirmed reports state that she has also taken son Zayed, seven, and daughter Al Jalila, 11, with her.
Princess Haya, 45, is half-sister of the King of Jordan.
She married Sheikh Mohammed in 2004 and is an accomplished show-jumper.
Sheikh Mohammed, 69, is vice-president and prime minister of the United Arab Emirates, as well as leader of the Emirate of Dubai.
He is believed to be worth £9 billion.
The end of his marriage is a fresh blow to the Sheik after one of his daughters – Princess Latifa bint Mohammed Maktoum, 33 – attempted to escape last year before being captured on a boat off the Indian coast.
Princess Latifa said abuse forced her to flee the kingdom – and human rights groups claim she is being held in captivity in Dubai.
She is reportedly seeking political asylum in Germany, having not been seen in public since February.
Radha Stirling, chief executive of watchdog Detained in Dubai, said: “Whenever someone applies for political asylum, obviously, it is because their lives are in danger, and because they have suffered severe abuses and violations of their human rights.
“We already know that Princess Latifa, Sheikh Mohammed’s daughter, fled the UAE seeking asylum and alleging unspeakable abuse at the hands of her father.
“Now, it seems, Princess Haya, Sheikh Mohammed’s wife, has also fled the country and sought refuge in Germany.”
She said there are now “serious questions” about what prompted Princess Haya – sister of the King of Jordan – to flee.
Reports in the Middle East claim Germany has refused a request to return the Sheikh’s wife.
According to sources close to the royal family, Princess Haya is hoping to secure a divorce from her wealthy husband – who last week attended Royal Ascot alone.
The Princess – who has not updated her social media accounts since February – usually accompanies her husband to the event.
German authorities have refused to comment on reports of Princess Haya’s escape from her husband.