Dr Rajan Daniel, hailing from Kerala, had been working at Ahalia Hospital since 2007. Last week his body was found on the floor of the hospital with a deep cut on his neck.
A man fleeing his room was nabbed by the hospital staff and handed over to the police.
Media reports said the attacker had been under Dr Daniel's observation for a urinary disease for several weeks and apparently visited the doctor for a follow-up. He was also said to be upset over the treatment of his ailment.
"It is unimaginable how a patient can murder the doctor even if the treatment has shown unsatisfactory results," an Indian doctor in Abu Dhabi said.
Some reports also suggest that the attacker blamed the doctor for the death of his relative.
A police official said the suspect was a Pakistani national and he was being interrogated by a special police team to establish the motive behind the crime, the Gulf News reported.
Meanwhile, arrangements are being made to send the victim's body to India.