The 69-year-old Sheikh Mohammed, a billionaire racehorse owner uploaded an angry poem on Instagram speaking about an unidentified woman of “treachery and betrayal”.
She became his sixth and “junior wife”. The Dubai ruler has 23 children by different wives.
Earlier this year, Princess Haya hid in Germany. Now she is living in a £85m town house in Kensington Palace Gardens, central London.
Princess Haya is preparing for a legal battle in the High Court.
Reports says Princess Haya is fleeing from her husband after she discovered disturbing facts behind the mysterious return to Dubai last year of Sheikha Latifa, one of the ruler’s daughters.
Sheikha Latifa fled the UAE with the help of a Frenchman by sea but was intercepted by armed men off the coast of India and returned to Dubai.
Princess Haya defended Dubai’s reputation over the incident along with former Irish president Mary Robinson.
Human rights advocates said Sheikha Latifa was forcibly abducted against her will while Dubai authorities said she had been “vulnerable to exploitation” and was “now safe in Dubai”
Ever since then it is alleged that Princess Haya discovered new facts about the incident and she consequently came under increasing hostility and pressure from members of her husband’s extended family until she no longer felt safe there.
Princess Haya fears that she may now be abducted herself and “rendered” back to Dubai.
The UAE embassy in London has declined to comment on what it says is a personal matter between two individuals.
Princess Haya, who was educated at Bryanston School in Dorset then Oxford University, is thought likely to want to stay in the UK.
If her estranged husband demands her return then this poses a diplomatic headache for Britain, which has close ties to the UAE.
The case is also awkward for Jordan since Princess Haya is the half-sister of Jordan’s King Abdullah. Nearly a quarter of a million Jordanians work in the UAE, sending back remittances, and Jordan cannot afford a rift with Dubai.